Methods for identifying a target site of a cas9 nuclease

ABSTRACT

Some aspects of this disclosure provide strategies, methods, and reagents for selecting a site-specific endonuclease based on determining its target site preferences and specificity. Methods and reagents for determining target site preference and specificity are also provided.

RELATED APPLICATION

This application claims priority under 35 U.S.C. §119(e) to U.S. provisional patent application, U.S. Ser. No. 61/864,289, filed Aug. 9, 2013, the entire contents of which are incorporated herein by reference.

GOVERNMENT SUPPORT

This invention was made with U.S. Government support under grant numbers HR0011-11-2-0003 and N66001-12-C-4207, awarded by the Defense Advanced Research Projects Agency. The U.S. Government has certain rights in the invention.

BACKGROUND OF THE INVENTION

Site-specific endonucleases theoretically allow for the targeted manipulation of a single site within a genome and are useful in the context of gene targeting as well as for therapeutic applications. In a variety of organisms, including mammals, site-specific endonucleases have been used for genome engineering by stimulating either non-homologous end joining or homologous recombination. In addition to providing powerful research tools, site-specific nucleases also have potential as gene therapy agents, and two site-specific endonucleases have recently entered clinical trials: one, CCR5-2246, targeting a human CCR-5 allele as part of an anti-HIV therapeutic approach (NCT00842634, NCT01044654, NCT01252641), and the other one, VF24684, targeting the human VEGF-A promoter as part of an anti-cancer therapeutic approach (NCT01082926).

Specific cleavage of the intended nuclease target site without or with only minimal off-target activity is a prerequisite for clinical applications of site-specific endonuclease, and also for high-efficiency genomic manipulations in basic research applications, as imperfect specificity of engineered site-specific binding domains has been linked to cellular toxicity and undesired alterations of genomic loci other than the intended target. Most nucleases available today, however, exhibit significant off-target activity, and thus may not be suitable for clinical applications. Technology for evaluating nuclease specificity and for engineering nucleases with improved specificity are therefore needed.

SUMMARY OF THE INVENTION

Some aspects of this disclosure are based on the recognition that the reported toxicity of some engineered site-specific endonucleases is based on off-target DNA cleavage, rather than on off-target binding alone. Some aspects of this disclosure provide strategies, compositions, systems, and methods to evaluate and characterize the sequence specificity of site-specific nucleases, for example, RNA-programmable endonucleases, such as Cas9 endonucleases, zinc finger nucleases (ZNFs), homing endonucleases, or transcriptional activator-like element nucleases (TALENs).

The strategies, methods, and reagents of the present disclosure represent, in some aspects, an improvement over previous methods for assaying nuclease specificity. For example, some previously reported methods for determining nuclease target site specificity profiles by screening libraries of nucleic acid molecules comprising candidate target sites relied on a “two-cut” in vitro selection method which requires indirect reconstruction of target sites from sequences of two half-sites resulting from two adjacent cuts of the nuclease of a library member nucleic acid (see e.g., PCT Application WO 2013/066438; and Pattanayak, V., Ramirez, C. L., Joung, J. K. & Liu, D. R. Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection. Nature methods 8, 765-770 (2011), the entire contents of each of which are incorporated herein by reference). In contrast to such “two-cut” strategies, the methods of the present disclosure utilize an optimized “one cut” screening strategy, which allows for the identification of library members that have been cut at least once by the nuclease. As explained in more detail elsewhere herein, the “one-cut” selection strategies provided herein are compatible with single end high-throughput sequencing methods and do not require computational reconstruction of cleaved target sites from cut half-sites, thus streamlining the nuclease profiling process.

Some aspects of this disclosure provide in vitro selection methods for evaluating the cleavage specificity of endonucleases and for selecting nucleases with a desired level of specificity. Such methods are useful, for example, for characterizing an endonuclease of interest and for identifying a nuclease exhibiting a desired level of specificity, for example, for identifying a highly specific endonuclease for clinical applications.

Some aspects of this disclosure provide methods of identifying suitable nuclease target sites that are sufficiently different from any other site within a genome to achieve specific cleavage by a given nuclease without any or at least minimal off-target cleavage. Such methods are useful for identifying candidate nuclease target sites that can be cleaved with high specificity on a genomic background, for example, when choosing a target site for genomic manipulation in vitro or in vivo.

Some aspects of this disclosure provide methods of evaluating, selecting, and/or designing site-specific nucleases with enhanced specificity as compared to current nucleases. For example, provided herein are methods that are useful for selecting and/or designing site-specific nucleases with minimal off-target cleavage activity, for example, by designing variant nucleases with binding domains having decreased binding affinity, by lowering the final concentration of the nuclease, by choosing target sites that differ by at least three base pairs from their closest sequence relatives in the genome, and, in the case of RNA-programmable nucleases, by selecting a guide RNA that results in the fewest off-target sites being bound and/or cut.

Compositions and kits useful in the practice of the methods described herein are also provided.

Some aspects of this disclosure provide methods for identifying a target site of a nuclease. In some embodiments, the method comprises (a) providing a nuclease that cuts a double-stranded nucleic acid target site, wherein cutting of the target site results in cut nucleic acid strands comprising a 5′ phosphate moiety; (b) contacting the nuclease of (a) with a library of candidate nucleic acid molecules, wherein each nucleic acid molecule comprises a concatemer of a sequence comprising a candidate nuclease target site and a constant insert sequence, under conditions suitable for the nuclease to cut a candidate nucleic acid molecule comprising a target site of the nuclease; and (c) identifying nuclease target sites cut by the nuclease in (b) by determining the sequence of an uncut nuclease target site on the nucleic acid strand that was cut by the nuclease in step (b). In some embodiments, the nuclease creates blunt ends. In some embodiments, the nuclease creates a 5′ overhang. In some embodiments, the determining of step (c) comprises ligating a first nucleic acid adapter to the 5′ end of a nucleic acid strand that was cut by the nuclease in step (b) via 5′-phosphate-dependent ligation. In some embodiments, the nucleic acid adapter is provided in double-stranded form. In some embodiments, the 5′-phosphate-dependent ligation is a blunt end ligation. In some embodiments, the method comprises filling in the 5′-overhang before ligating the first nucleic acid adapter to the nucleic acid strand that was cut by the nuclease. In some embodiments, the determining of step (c) further comprises amplifying a fragment of the concatemer cut by the nuclease that comprises an uncut target site via a PCR reaction using a PCR primer that hybridizes with the adapter and a PCR primer that hybridizes with the constant insert sequence. In some embodiments, the method further comprises enriching the amplified nucleic acid molecules for molecules comprising a single uncut target sequence. In some embodiments, the step of enriching comprises a size fractionation. In some embodiments, the determining of step (c) comprises sequencing the nucleic acid strand that was cut by the nuclease in step (b), or a copy thereof obtained via PCR. In some embodiments, the library of candidate nucleic acid molecules comprises at least 10⁸, at least 10⁹, at least 10¹⁰, at least 10¹¹, or at least 10¹² different candidate nuclease cleavage sites. In some embodiments, the nuclease is a therapeutic nuclease which cuts a specific nuclease target site in a gene associated with a disease. In some embodiments, the method further comprises determining a maximum concentration of the therapeutic nuclease at which the therapeutic nuclease cuts the specific nuclease target site, and does not cut more than 10, more than 5, more than 4, more than 3, more than 2, more than 1, or no additional nuclease target sites. In some embodiments, the method further comprises administering the therapeutic nuclease to a subject in an amount effective to generate a final concentration equal or lower than the maximum concentration. In some embodiments, the nuclease is an RNA-programmable nuclease that forms a complex with an RNA molecule, and wherein the nuclease:RNA complex specifically binds a nucleic acid sequence complementary to the sequence of the RNA molecule. In some embodiments, the RNA molecule is a single-guide RNA (sgRNA). In some embodiments, the sgRNA comprises 5-50 nucleotides, 10-30 nucleotides, 15-25 nucleotides, 18-22 nucleotides, 19-21 nucleotides, e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, the nuclease is a Cas9 nuclease. In some embodiments, the nuclease target site comprises a [sgRNA-complementary sequence]-[protospacer adjacent motif (PAM)] structure, and the nuclease cuts the target site within the sgRNA-complementary sequence. In some embodiments, the sgRNA-complementary sequence comprises 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, the nuclease comprises an unspecific nucleic acid cleavage domain. In some embodiments, the nuclease comprises a FokI cleavage domain. In some embodiments, the nuclease comprises a nucleic acid cleavage domain that cleaves a target sequence upon cleavage domain dimerization. In some embodiments, the nuclease comprises a binding domain that specifically binds a nucleic acid sequence. In some embodiments, the binding domain comprises a zinc finger. In some embodiments, the binding domain comprises at least 2, at least 3, at least 4, or at least 5 zinc fingers. In some embodiments, the nuclease is a Zinc Finger Nuclease. In some embodiments, the binding domain comprises a Transcriptional Activator-Like Element. In some embodiments, the nuclease is a Transcriptional Activator-Like Element Nuclease (TALEN). In some embodiments, the nuclease is an organic compound. In some embodiments, the nuclease comprises an enediyne functional group. In some embodiments, the nuclease is an antibiotic. In some embodiments, the compound is dynemicin, neocarzinostatin, calicheamicin, esperamicin, bleomycin, or a derivative thereof. In some embodiments, the nuclease is a homing endonuclease.

Some aspects of this disclosure provide libraries of nucleic acid molecules, in which each nucleic acid molecule comprises a concatemer of a sequence comprising a candidate nuclease target site and a constant insert sequence of 10-100 nucleotides. In some embodiments, the constant insert sequence is at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, or at least 95 nucleotides long. In some embodiments, the constant insert sequence is not more than 15, not more than 20, not more than 25, not more than 30, not more than 35, not more than 40, not more than 45, not more than 50, not more than 55, not more than 60, not more than 65, not more than 70, not more than 75, not more than 80, or not more than 95 nucleotides long. In some embodiments, the candidate nuclease target sites are sites that can be cleaved by an RNA-programmable nuclease, a Zinc Finger Nuclease (ZFN), a Transcription Activator-Like Effector Nuclease (TALEN), a homing endonuclease, an organic compound nuclease, or an enediyne antibiotic (e.g., dynemicin, neocarzinostatin, calicheamicin, esperamicin, bleomycin). In some embodiments, the candidate nuclease target site can be cleaved by a Cas9 nuclease. In some embodiments, the library comprises at least 10⁵, at least 10⁶, at least 10⁷, at least 10⁸, at least 10⁹, at least 10¹⁰, at least 10¹¹, or at least 10¹² different candidate nuclease target sites. In some embodiments, the library comprises nucleic acid molecules of a molecular weight of at least 0.5 kDa, at least 1 kDa, at least 2 kDa, at least 3 kDa, at least 4 kDa, at least 5 kDa, at least 6 kDa, at least 7 kDa, at least 8 kDa, at least 9 kDa, at least 10 kDa, at least 12 kDa, or at least 15 kDa. In some embodiments, the library comprises candidate nuclease target sites that are variations of a known target site of a nuclease of interest. In some embodiments, the variations of a known nuclease target site comprise 10 or fewer, 9 or fewer, 8 or fewer, 7 or fewer, 6 or fewer, 5 or fewer, 4 or fewer, 3 or fewer, or 2 or fewer mutations as compared to a known nuclease target site. In some embodiments, the variations differ from the known target site of the nuclease of interest by more than 5%, more than 10%, more than 15%, more than 20%, more than 25%, or more than 30% on average, distributed binomially. In some embodiments, the variations differ from the known target site by no more than 10%, no more than 15%, no more than 20%, no more than 25%, nor more than 30%, no more than 40%, or no more than 50% on average, distributed binomially. In some embodiments, the nuclease of interest is a Cas9 nuclease, a zinc finger nuclease, a TALEN, a homing endonuclease, an organic compound nuclease, or an enediyne antibiotic (e.g., dynemicin, neocarzinostatin, calicheamicin, esperamicin, bleomycin). In some embodiments, the candidate nuclease target sites are Cas9 nuclease target sites that comprise a [sgRNA-complementary sequence]-[PAM] structure, wherein the sgRNA-complementary sequence comprises 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.

Some aspects of this disclosure provide methods for selecting a nuclease that specifically cuts a consensus target site from a plurality of nucleases. In some embodiments, the method comprises (a) providing a plurality of candidate nucleases that cut the same consensus sequence; (b) for each of the candidate nucleases of step (a), identifying a nuclease target site cleaved by the candidate nuclease that differ from the consensus target site using a method provided herein; (c) selecting a nuclease based on the nuclease target site(s) identified in step (b). In some embodiments, the nuclease selected in step (c) is the nuclease that cleaves the consensus target site with the highest specificity. In some embodiments, the nuclease that cleaves the consensus target site with the highest specificity is the candidate nuclease that cleaves the lowest number of target sites that differ from the consensus site. In some embodiments, the candidate nuclease that cleaves the consensus target site with the highest specificity is the candidate nuclease that cleaves the lowest number of target sites that are different from the consensus site in the context of a target genome. In some embodiments, the candidate nuclease selected in step (c) is a nuclease that does not cleave any target site other than the consensus target site. In some embodiments, the candidate nuclease selected in step (c) is a nuclease that does not cleave any target site other than the consensus target site within the genome of a subject at a therapeutically effective concentration of the nuclease. In some embodiments, the method further comprises contacting a genome with the nuclease selected in step (c). In some embodiments, the genome is a vertebrate, mammalian, human, non-human primate, rodent, mouse, rat, hamster, goat, sheep, cattle, dog, cat, reptile, amphibian, fish, nematode, insect, or fly genome. In some embodiments, the genome is within a living cell. In some embodiments, the genome is within a subject. In some embodiments, the consensus target site is within an allele that is associated with a disease or disorder. In some embodiments, cleavage of the consensus target site results in treatment or prevention of a disease or disorder, e.g., amelioration or prevention of at least one sign and/or symptom of the disease or disorder. In some embodiments, cleavage of the consensus target site results in the alleviation of a sign and/or symptom of the disease or disorder. In some embodiments, cleavage of the consensus target site results in the prevention of the disease or disorder. In some embodiments, the disease is HIV/AIDS. In some embodiments, the allele is a CCR5 allele. In some embodiments, the disease is a proliferative disease. In some embodiments, the disease is cancer. In some embodiments, the allele is a VEGFA allele.

Some aspects of this disclosure provide isolated nucleases that have been selected according to a method provided herein. In some embodiments, the nuclease has been engineered to cleave a target site within a genome. In some embodiments, the nuclease is a Cas9 nuclease comprising an sgRNA that is complementary to the target site within the genome. In some embodiments, the nuclease is a Zinc Finger Nuclease (ZFN) or a Transcription Activator-Like Effector Nuclease (TALEN), a homing endonuclease, or an organic compound nuclease (e.g., an enediyne, an antibiotic nuclease, dynemicin, neocarzinostatin, calicheamicin, esperamicin, bleomycin, or a derivative thereof). In some embodiments, the nuclease has been selected based on cutting no other candidate target site, not more than one candidate target site, not more than two candidate target sites, not more than three candidate target sites, not more than four candidate target sites, not more than five candidate target sites, not more than six candidate target sites, not more than seven candidate target sites, not more than eight candidate target sites, not more than eight candidate target sites, not more than nine candidate target sites, or not more than ten candidate target sites in addition to its known nuclease target site.

Some aspects of this disclosure provide kits comprising a library of nucleic acid molecules comprising candidate nuclease target sites as provided herein. Some aspects of this disclosure provide kits comprising an isolated nuclease as provided herein. In some embodiments, the nuclease is a Cas9 nuclease. In some embodiments, the kit further comprises a nucleic acid molecule comprising a target site of the isolated nuclease. In some embodiments, the kit comprises an excipient and instructions for contacting the nuclease with the excipient to generate a composition suitable for contacting a nucleic acid with the nuclease. In some embodiments, the composition is suitable for contacting a nucleic acid within a genome. In some embodiments, the composition is suitable for contacting a nucleic acid within a cell. In some embodiments, the composition is suitable for contacting a nucleic acid within a subject. In some embodiments, the excipient is a pharmaceutically acceptable excipient.

Some aspects of this disclosure provide pharmaceutical compositions that are suitable for administration to a subject. In some embodiments, the composition comprises an isolated nuclease as provided herein. In some embodiments, the composition comprises a nucleic acid encoding such a nuclease. In some embodiments, the composition comprises a pharmaceutically acceptable excipient.

Other advantages, features, and uses of the invention will be apparent from the detailed description of certain non-limiting embodiments of the invention; the drawings, which are schematic and not intended to be drawn to scale; and the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-B. In vitro selection overview. (a) Cas9 complexed with a short guide RNA (sgRNA) recognizes ˜20 bases of a target DNA substrate that is complementary to the sgRNA sequence and cleaves both DNA strands. The white triangles represent cleavage locations. (b) A modified version of our previously described in vitro selection was used to comprehensively profile Cas9 specificity. A concatemeric pre-selection DNA library in which each molecule contains one of 10¹² distinct variants of a target DNA sequence (white rectangles) was generated from synthetic DNA oligonucleotides by ligation and rolling-circle amplification. This library was incubated with a Cas9:sgRNA complex of interest. Cleaved library members contain 5′ phosphate groups (circles) and therefore are substrates for adapter ligation and PCR. The resulting amplicons were subjected to high-throughput DNA sequencing and computational analysis.

FIGS. 2A-H. In vitro selection results for Cas9:CLTA1 sgRNA. Heat maps²¹ show the specificity profiles of Cas9:CLTA1 sgRNA v2.1 under enzyme-limiting conditions (a, b), Cas9:CLTA1 sgRNA v1.0 under enzyme-saturating conditions (c, d), and Cas9:CLTA1 sgRNA v2.1 under enzyme-saturating conditions (e, f). Heat maps show all post-selection sequences (a, c, e) or only those sequences containing a single mutation in the 20-base pair sgRNA-specified target site and two-base pair PAM (b, d, f). Specificity scores of 1.0 and −1.0 corresponds to 100% enrichment for and against, respectively, a particular base pair at a particular position. Black boxes denote the intended target nucleotides. (g) Effect of Cas9:sgRNA concentration on specificity. Positional specificity changes between enzyme-limiting (200 nM DNA, 100 nM Cas9:sgRNA v2.1) and enzyme-saturating (200 nM DNA, 1000 nM Cas9:sgRNA v2.1) conditions, normalized to the maximum possible change in positional specificity, are shown for CLTA1. (h) Effect of sgRNA architecture on specificity. Positional specificity changes between sgRNA v1.0 and sgRNA v2.1 under enzyme-saturating conditions, normalized to the maximum possible change in positional specificity, are shown for CLTA1. See FIGS. 6-8, 25, and 26 for corresponding data for CLTA2, CLTA3, and CLTA4.

FIGS. 3A-D. Target sites profiled in this study. (A) The 5′ end of the sgRNA has 20 nucleotides that are complementary to the target site. The target site contains an NGG motif (PAM) adjacent to the region of RNA:DNA complementarity. (B) Four human clathrin gene (CLTA) target sites are shown. (C, D) Four human clathrin gene (CLTA) target sites are shown with sgRNAs. sgRNA v1.0 is shorter than sgRNA v2.1. The PAM is shown for each site. The non-PAM end of the target site corresponds to the 5′ end of the sgRNA.

FIG. 4. Cas9:guide RNA cleavage of on-target DNA sequences in vitro. Discrete DNA cleavage assays on an approximately 1-kb linear substrate were performed with 200 nM on-target site and 100 nM Cas9:v1.0 sgRNA, 100 nM Cas9:v2.1 sgRNA, 1000 nM Cas9:v1.0 sgRNA, and 1000 nM Cas9:v2.1 sgRNA for each of four CLTA target sites. For CLTA1, CLTA2, and CLTA4, Cas9:v2.1 sgRNA shows higher activity than Cas9:v1.0 sgRNA. For CLTA3, the activities of the Cas9:v1.0 sgRNA and Cas9:v2.1 sgRNA were comparable.

FIGS. 5A-E. In vitro selection results for four target sites. In vitro selections were performed on 200 nM pre-selection library with 100 nM Cas9:sgRNA v2.1, 1000 nM Cas9:sgRNA v1.0, or 1000 nM Cas9:sgRNA v2.1. (A) Post-selection PCR products are shown for the 12 selections performed. DNA containing 1.5 repeats were quantified for each selection and pooled in equimolar amounts before gel purification and sequencing. (B-E) Distributions of mutations are shown for pre-selection (black) and post-selection libraries (colored). The post-selection libraries are enriched for sequences with fewer mutations than the pre-selection libraries. Mutations are counted from among the 20 base pairs specified by the sgRNA and the two-base pair PAM. P-values are <0.01 for all pairwise comparisons between distributions in each panel. P-values were calculated using t-tests, assuming unequal size and unequal variance.

FIGS. 6A-F. In vitro selection results for Cas9:CLTA2 sgRNA. Heat maps²⁴ show the specificity profiles of Cas9:CLTA2 sgRNA v2.1 under enzyme-limiting conditions (A, B), Cas9:CLTA2 sgRNA v1.0 under enzyme-excess conditions (C, D), and Cas9:CLTA2 sgRNA v2.1 under enzyme-excess conditions (E, F). Heat maps show all post-selection sequences (A, C, E) or only those sequences containing a single mutation in the 20-base pair sgRNA-specified target site and two-base pair PAM (B, D, F). Specificity scores of 1.0 and −1.0 corresponds to 100% enrichment for and against, respectively, a particular base pair at a particular position. Black boxes denote the intended target nucleotides.

FIGS. 7A-F. In vitro selection results for Cas9:CLTA3 sgRNA. Heat maps²⁴ show the specificity profiles of Cas9:CLTA3 sgRNA v2.1 under enzyme-limiting conditions (A, B), Cas9:CLTA3 sgRNA v1.0 under enzyme-excess conditions (C, D), and Cas9:CLTA3 sgRNA v2.1 under enzyme-saturating conditions (E, F). Heat maps show all post-selection sequences (A, C, E) or only those sequences containing a single mutation in the 20-base pair sgRNA-specified target site and two-base pair PAM (B, D, F). Specificity scores of 1.0 and −1.0 corresponds to 100% enrichment for and against, respectively, a particular base pair at a particular position. Black boxes denote the intended target nucleotides.

FIGS. 8A-F. In vitro selection results for Cas9:CLTA4 sgRNA. Heat maps²⁴ show the specificity profiles of Cas9:CLTA4 sgRNA v2.1 under enzyme-limiting conditions (A, B), Cas9:CLTA4 sgRNA v1.0 under enzyme-excess conditions (C, D), and Cas9:CLTA4 sgRNA v2.1 under enzyme-saturating conditions (E, F). Heat maps show all post-selection sequences (A, C, E) or only those sequences containing a single mutation in the 20-base pair sgRNA-specified target site and two-base pair PAM (B, D, F). Specificity scores of 1.0 and −1.0 corresponds to 100% enrichment for and against, respectively, a particular base pair at a particular position. Black boxes denote the intended target nucleotides.

FIGS. 9A-D. In vitro selection results as sequence logos. Information content is plotted²⁵ for each target site position (1-20) specified by CLTA1 (A), CLTA2 (B), CLTA3 (C), and CLTA4 (D) sgRNA v2.1 under enzyme-limiting conditions. Positions in the PAM are labelled “P1,” “P2,” and “P3.” Information content is plotted in bits. 2.0 bits indicates absolute specificity and 0 bits indicates no specificity.

FIGS. 10A-L. Tolerance of mutations distal to the PAM for CLTA1. The maximum specificity scores at each position are shown for the Cas9:CLTA1 v2.1 sgRNA selections when considering only those sequences with on-target base pairs in gray, while allowing mutations in the first 1-12 base pairs (a-l). The positions that are not constrained to on-target base pairs are indicated by dark bars. Higher specificity score values indicate higher specificity at a given position. The positions that were not allowed to contain any mutations (gray) were plotted with a specificity score of +1. For all panels, specificity scores were calculated from pre-selection library sequences and post-selection library sequences with an n≧5,130 and n≧74,538, respectively.

FIGS. 11A-L. Tolerance of mutations distal to the PAM for CLTA2. The maximum specificity scores at each position are shown for the Cas9:CLTA2 v2.1 sgRNA selections when considering only those sequences with on-target base pairs in gray, while allowing mutations in the first 1-12 base pairs (a-l). The positions that are not constrained to on-target base pairs are indicated by dark bars. Higher specificity score values indicate higher specificity at a given position. The positions that were not allowed to contain any mutations (gray) were plotted with a specificity score of +1. For all panels, specificity scores were calculated from pre-selection library sequences and post-selection library sequences with an n≧3,190 and n≧25,365, respectively.

FIGS. 12A-L. Tolerance of mutations distal to the PAM for CLTA3. The maximum specificity scores at each position are shown for the Cas9:CLTA3 v2.1 sgRNA selections when considering only those sequences with on-target base pairs in gray, while allowing mutations in the first 1-12 base pairs (a-l). The positions that are not constrained to on-target base pairs are indicated by dark bars. Higher specificity score values indicate higher specificity at a given position. The positions that were not allowed to contain any mutations (gray) were plotted with a specificity score of +1. For all panels, specificity scores were calculated from pre-selection library sequences and post-selection library sequences with an n≧5,604 and n≧158,424, respectively.

FIGS. 13A-I. Tolerance of mutations distal to the PAM for CLTA4. The maximum specificity scores at each position are shown for the Cas9:CLTA4 v2.1 sgRNA selections when considering only those sequences with on-target base pairs in gray, while allowing mutations in the first 1-12 base pairs (a-i). The positions that are not constrained to on-target base pairs are indicated by dark bars. Higher specificity score values indicate higher specificity at a given position. The positions that were not allowed to contain any mutations (gray) were plotted with a specificity score of +1. For all panels, specificity scores were calculated from pre-selection library sequences and post-selection library sequences with an n≧2,323 and n≧21,819, respectively.

FIGS. 14A-L. Tolerance of mutations distal to the PAM in CLTA1 target sites. Distributions of mutations are shown for in vitro selection on 200 nM pre-selection library with 1000 nM Cas9:CLTA1 sgRNA v2.1. The number of mutations shown are in a 1-12 base pair target site subsequence farthest from the PAM (a-l) when the rest of the target site, including the PAM, contains only on-target base pairs. The pre-selection and post-selection distributions are similar for up to three base pairs, demonstrating tolerance for target sites with mutations in the three base pairs farthest from the PAM when the rest of the target sites have optimal interactions with the Cas9:sgRNA. For all panels, graphs were generated from pre-selection library sequences and post-selection library sequences with an n≧5,130 and n≧74,538, respectively.

FIGS. 15A-L. Tolerance of mutations distal to the PAM in CLTA2 target sites. Distributions of mutations are shown for in vitro selection on 200 nM pre-selection library with 1000 nM Cas9:CLTA2 sgRNA v2.1. The number of mutations shown are in a 1-12 base pair target site subsequence farthest from the PAM (a-l) when the rest of the target site, including the PAM, contains only on-target base pairs. The pre-selection and post-selection distributions are similar for up to three base pairs, demonstrating tolerance for target sites with mutations in the three base pairs farthest from the PAM when the rest of the target sites have optimal interactions with the Cas9:sgRNA. For all panels, graphs were generated from pre-selection library sequences and post-selection library sequences with an n≧3,190 and n≧21,265, respectively.

FIGS. 16A-L. Tolerance of mutations distal to PAM in CLTA3 target sites. Distributions of mutations are shown for in vitro selection on 200 nM pre-selection library with 1000 nM Cas9:CLTA3 sgRNA v2.1. The number of mutations shown are in a 1-12 base pair target site subsequence farthest from the PAM (a-l) when the rest of the target site, including the PAM, contains only on-target base pairs. The pre-selection and post-selection distributions are similar for up to three base pairs, demonstrating tolerance for target sites with mutations in the three base pairs farthest from the PAM when the rest of the target sites have optimal interactions with the Cas9:sgRNA. For all panels, graphs were generated from pre-selection library sequences and post-selection library sequences with an n≧5,604 and n≧158,424, respectively.

FIGS. 17A-L. Tolerance of mutations distal to PAM in CLTA4 target sites. Distributions of mutations are shown for in vitro selection on 200 nM pre-selection library with 1000 nM Cas9:CLTA4 sgRNA v2.1. The number of mutations shown are in a 1-12 base pair target site subsequence farthest from the PAM (a-l) when the rest of the target site, including the PAM, contains only on-target base pairs. The pre-selection and post-selection distributions are similar for up to three base pairs, demonstrating tolerance for target sites with mutations in the three base pairs farthest from the PAM when the rest of the target sites have optimal interactions with the Cas9:sgRNA. For all panels, graphs were generated from pre-selection library sequences and post-selection library sequences with an n≧2,323 and n≧21,819, respectively.

FIGS. 18A-D. Positional specificity patterns for 100 nM Cas9:sgRNA v2.1. Positional specificity, defined as the sum of the magnitude of the specificity score for each of the four possible base pairs recognized at a certain position in the target site, is plotted for each target site under enzyme-limiting conditions for sgRNA v2.1 (A-D). The positional specificity is shown as a value normalized to the maximum positional specificity value of the target site. Positional specificity is highest at the end of the target site proximal to the PAM and is lowest in the middle of the target site and in the several nucleotides most distal to the PAM.

FIGS. 19A-D. Positional specificity patterns for 1000 nM Cas9:sgRNA v1.0. Positional specificity, defined as the sum of the magnitude of the specificity score for each of the four possible base pairs recognized at a certain position in the target site, is plotted for each target site under enzyme-excess conditions with sgRNA v1.0 (A-D). The positional specificity is shown as a value normalized to the maximum positional specificity value of the target site. Positional specificity is relatively constant across the target site but is lowest in the middle of the target site and in the several nucleotides most distal to the PAM.

FIGS. 20A-D. Positional specificity patterns for 1000 nM Cas9:sgRNA v2.1. Positional specificity, defined as the sum of the magnitude of the specificity score for each of the four possible base pairs recognized at a certain position in the target site, is plotted for each target site under enzyme-excess conditions with sgRNA v2.1 (A-D). The positional specificity is shown as a value normalized to the maximum positional specificity value of the target site. Positional specificity is relatively constant across the target site but is lowest in the middle of the target site and in the several nucleotides most distal to the PAM.

FIGS. 21A-D. PAM nucleotide preferences. The abundance in the pre-selection library and post-selection libraries under enzyme-limiting or enzyme-excess conditions are shown for all 16 possible PAM dinucleotides for selections with CLTA1 (a), CLTA2 (b), CLTA3 (c), and CLTA4 (d) sgRNA v2.1. GG dinucleotides increased in abundance in the post-selection libraries, while the other possible PAM dinucleotides decreased in abundance after the selection.

FIGS. 22A-D. PAM nucleotide preferences for on-target sites. Only post-selection library members containing no mutations in the 20 base pairs specified by the guide RNAs were included in this analysis. The abundance in the pre-selection library and post-selection libraries under enzyme-limiting and enzyme-excess conditions are shown for all 16 possible PAM dinucleotides for selections with CLTA1 (A), CLTA2 (B), CLTA3 (C), and CLTA4 (D) sgRNA v2.1. GG dinucleotides increased in abundance in the post-selection libraries, while the other possible PAM dinucleotides generally decreased in abundance after the selection, although this effect for the enzyme-excess concentrations of Cas9:sgRNA was modest or non-existent for many dinucleotides.

FIGS. 23A-D. PAM dinucleotide specificity scores. The specificity scores under enzyme-limiting and enzyme-excess conditions are shown for all 16 possible PAM dinucleotides (positions 2 and 3 of the three-nucleotide NGG PAM) for selections with CLTA1 (A), CLTA2 (B), CLTA3 (C), and CLTA4 (D) sgRNA v2.1. The specificity score indicates the enrichment of the PAM dinucleotide in the post-selection library relative to the pre-selection library, normalized to the maximum possible enrichment of that dinucleotide. A specificity score of +1.0 indicates that a dinucleotide is 100% enriched in the post-selection library, and a specificity score of −1.0 indicates that a dinucleotide is 100% de-enriched. GG dinucleotides were the most enriched in the post-selection libraries, and AG, GA, GC, GT, and TG show less relative de-enrichment compared to the other possible PAM dinucleotides.

FIGS. 24A-D. PAM dinucleotide specificity scores for on-target sites. Only post-selection library members containing no mutations in the 20 base pairs specified by the guide RNAs were included in this analysis. The specificity scores under enzyme-limiting and enzyme-excess conditions are shown for all 16 possible PAM dinucleotides (positions 2 and 3 of the three-nucleotide NGG PAM) for selections with CLTA1 (A), CLTA2 (B), CLTA3 (C), and CLTA4 (D) sgRNA v2.1. The specificity score indicates the enrichment of the PAM dinucleotide in the post-selection library relative to the pre-selection library, normalized to the maximum possible enrichment of that dinucleotide. A specificity score of +1.0 indicates that a dinucleotide is 100% enriched in the post-selection library, and a specificity score of −1.0 indicates that a dinucleotide is 100% de-enriched. GG dinucleotides were the most enriched in the post-selection libraries, AG and GA nucleotides were neither enriched or de-enriched in at least one selection condition, and GC, GT, and TG show less relative de-enrichment compared to the other possible PAM dinucleotides.

FIGS. 25A-D. Effects of Cas9:sgRNA concentration on specificity. Positional specificity changes between enzyme-limiting (200 nM DNA, 100 nM Cas9:sgRNA v2.1) and enzyme-excess (200 nM DNA, 1000 nM Cas9:sgRNA v2.1) conditions are shown for selections with sgRNAs targeting CLTA1 (A), CLTA2 (B), CLTA3 (C), and CLTA4 (D) target sites. Lines indicate the maximum possible change in positional specificity for a given position. The highest changes in specificity occur proximal to the PAM as enzyme concentration is increased.

FIGS. 26A-D. Effects of sgRNA architecture on specificity. Positional specificity changes between Cas9:sgRNA v1.0 and Cas9:sgRNA v2.1 under enzyme-excess (200 nM DNA, 1000 nM Cas9:sgRNA v2.1) conditions are shown for selections with sgRNAs targeting CLTA1 (A), CLTA2 (B), CLTA3 (C), and CLTA4 (D) target sites. Lines indicate the maximum possible change in positional specificity for a given position.

FIG. 27. Cas9:guide RNA cleavage of off-target DNA sequences in vitro. Discrete DNA cleavage assays on a 96-bp linear substrate were performed with 200 nM DNA and 1000 nM Cas9:CLTA4 v2.1 sgRNA for the on-target CLTA4 site (CLTA4-0) and five CLTA4 off-target sites identified by in vitro selection. Enrichment values shown are from the in vitro selection with 1000 nM Cas9:CLTA4 v2.1 sgRNA. CLTA4-1 and CLTA4-3 were the most highly enriched sequences under these conditions. CLTA4-2a, CLTA4-2b, and CLTA4-2c are two-mutation sequences that represent a range of enrichment values from high enrichment to no enrichment to high de-enrichment. Lowercase letters indicate mutations relative to the on-target CLTA4 site. The enrichment values are qualitatively consistent with the observed amount of cleavage in vitro.

FIG. 28. Effect of guide RNA architecture and Cas9:sgRNA concentration on in vitro cleavage of an off-target site. Discrete DNA cleavage assays on a 96-bp linear substrate were performed with 200 nM DNA and 100 nM Cas9:v1.0 sgRNA, 100 nM Cas9:v2.1 sgRNA, 1000 nM Cas9:v1.0 sgRNA, or 1000 nM Cas9:v2.1 sgRNA for the CLTA4-3 off-target site (5′ GggGATGTAGTGTTTCCACtGGG—mutations are shown in lowercase letters). DNA cleavage is observed under all four conditions tested, and cleavage rates are higher under enzyme-excess conditions, or with v2.1 sgRNA compared with v1.0 sgRNA.

DEFINITIONS

As used herein and in the claims, the singular forms “a,” “an,” and “the” include the singular and the plural reference unless the context clearly indicates otherwise. Thus, for example, a reference to “an agent” includes a single agent and a plurality of such agents.

The term “Cas9” or “Cas9 nuclease” refers to an RNA-guided nuclease comprising a Cas9 protein, or a fragment thereof. A Cas9 nuclease is also referred to sometimes as a casnI nuclease or a CRISPR (clustered regularly interspaced short palindromic repeat)-associated nuclease. CRISPR is an adaptive immune system that provides protection against mobile genetic elements (e.g., viruses, transposable elements and conjugative plasmids). CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). In type II CRISPR systems correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (mc) and a Cas9 protein. The tracrRNA serves as a guide for ribonuclease 3-aided processing of pre-crRNA. Subsequently, Cas9/crRNA/tracrRNA endonucleolytically cleaves linear or circular dsDNA target complementary to the spacer. The target strand not complementary to crRNA is first cut endonucleolytically, then trimmed 3′-5′ exonucleolytically. In nature, DNA-binding and cleavage typically requires protein and both RNA species. However, single guide RNAs (“sgRNA”, or simply “gNRA”) can be engineered so as to incorporate aspects of both the crRNA and tracrRNA into a single RNA molecule. See, e.g., Jinek M., Chylinski K., Fonfara I., Hauer M., Doudna J. A., Charpentier E. Science 337:816-821(2012), the entire contents of which is hereby incorporated by reference. Cas9 recognizes a short motif in the CRISPR repeat sequences (the PAM or protospacer adjacent motif) to help distinguish self versus non-self. Cas9 nuclease sequences and structures are well known to those of skill in the art (see, e.g., “Complete genome sequence of an M1 strain of Streptococcus pyogenes.” Ferretti J. J., McShan W. M., Ajdic D. J., Savic D. J., Savic G., Lyon K., Primeaux C., Sezate S., Suvorov A. N., Kenton S., Lai H. S., Lin S. P., Qian Y., Jia H. G., Najar F. Z., Ren Q., Zhu H., Song L. expand/collapse author list McLaughlin R. E., Proc. Natl. Acad. Sci. U.S.A. 98:4658-4663(2001); “CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III.” Deltcheva E., Chylinski K., Sharma C. M., Gonzales K., Chao Y., Pirzada Z. A., Eckert M. R., Vogel J., Charpentier E., Nature 471:602-607(2011); and “A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.” Jinek M., Chylinski K., Fonfara I., Hauer M., Doudna J. A., Charpentier E. Science 337:816-821(2012), the entire contents of each of which are incorporated herein by reference). Cas9 orthologs have been described in various species, including, but not limited to, S. pyogenes and S. thermophilus. Additional suitable Cas9 nucleases and sequences will be apparent to those of skill in the art based on this disclosure, and such Cas9 nucleases and sequences include Cas9 sequences from the organisms and loci disclosed in Chylinski, Rhun, and Charpentier, “The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems” (2013) RNA Biology 10:5, 726-737; the entire contents of which are incorporated herein by reference. In some embodiments, proteins comprising Cas9 or fragments thereof proteins are referred to as “Cas9 variants.” A Cas9 variant shares homology to Cas9, or a fragment thereof. For example a Cas9 variant is at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% to wild type Cas9. In some embodiments, the Cas9 variant comprises a fragment of Cas9 (e.g., a gRNA binding domain or a DNA-cleavage domain), such that the fragment is at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% to the corresponding fragment of wild type Cas9. In some embodiments, wild type Cas9 corresponds to Cas9 from Streptococcus pyogenes (NCBI Reference Sequence: NC_(—)017053.1, SEQ ID NO:40 (nucleotide); SEQ ID NO:41 (amino acid)).

(SEQ ID NO: 40) ATGGATAAGAAATACTCAATAGGCTTAGATATCGGCACAAATAGCGTCGG ATGGGCGGTGATCACTGATGATTATAAGGTTCCGTCTAAAAAGTTCAAGG TTCTGGGAAATACAGACCGCCACAGTATCAAAAAAAATCTTATAGGGGCT CTTTTATTTGGCAGTGGAGAGACAGCGGAAGCGACTCGTCTCAAACGGAC AGCTCGTAGAAGGTATACACGTCGGAAGAATCGTATTTGTTATCTACAGG AGATTTTTTCAAATGAGATGGCGAAAGTAGATGATAGTTTCTTTCATCGA CTTGAAGAGTCTTTTTTGGTGGAAGAAGACAAGAAGCATGAACGTCATCC TATTTTTGGAAATATAGTAGATGAAGTTGCTTATCATGAGAAATATCCAA CTATCTATCATCTGCGAAAAAAATTGGCAGATTCTACTGATAAAGCGGAT TTGCGCTTAATCTATTTGGCCTTAGCGCATATGATTAAGTTTCGTGGTCA TTTTTTGATTGAGGGAGATTTAAATCCTGATAATAGTGATGTGGACAAAC TATTTATCCAGTTGGTACAAATCTACAATCAATTATTTGAAGAAAACCCT ATTAACGCAAGTAGAGTAGATGCTAAAGCGATTCTTTCTGCACGATTGAG TAAATCAAGACGATTAGAAAATCTCATTGCTCAGCTCCCCGGTGAGAAGA GAAATGGCTTGTTTGGGAATCTCATTGCTTTGTCATTGGGATTGACCCCT AATTTTAAATCAAATTTTGATTTGGCAGAAGATGCTAAATTACAGCTTTC AAAAGATACTTACGATGATGATTTAGATAATTTATTGGCGCAAATTGGAG ATCAATATGCTGATTTGTTTTTGGCAGCTAAGAATTTATCAGATGCTATT TTACTTTCAGATATCCTAAGAGTAAATAGTGAAATAACTAAGGCTCCCCT ATCAGCTTCAATGATTAAGCGCTACGATGAACATCATCAAGACTTGACTC TTTTAAAAGCTTTAGTTCGACAACAACTTCCAGAAAAGTATAAAGAAATC TTTTTTGATCAATCAAAAAACGGATATGCAGGTTATATTGATGGGGGAGC TAGCCAAGAAGAATTTTATAAATTTATCAAACCAATTTTAGAAAAAATGG ATGGTACTGAGGAATTATTGGTGAAACTAAATCGTGAAGATTTGCTGCGC AAGCAACGGACCTTTGACAACGGCTCTATTCCCCATCAAATTCACTTGGG TGAGCTGCATGCTATTTTGAGAAGACAAGAAGACTTTTATCCATTTTTAA AAGACAATCGTGAGAAGATTGAAAAAATCTTGACTTTTCGAATTCCTTAT TATGTTGGTCCATTGGCGCGTGGCAATAGTCGTTTTGCATGGATGACTCG GAAGTCTGAAGAAACAATTACCCCATGGAATTTTGAAGAAGTTGTCGATA AAGGTGCTTCAGCTCAATCATTTATTGAACGCATGACAAACTTTGATAAA AATCTTCCAAATGAAAAAGTACTACCAAAACATAGTTTGCTTTATGAGTA TTTTACGGTTTATAACGAATTGACAAAGGTCAAATATGTTACTGAGGGAA TGCGAAAACCAGCATTTCTTTCAGGTGAACAGAAGAAAGCCATTGTTGAT TTACTCTTCAAAACAAATCGAAAAGTAACCGTTAAGCAATTAAAAGAAGA TTATTTCAAAAAAATAGAATGTTTTGATAGTGTTGAAATTTCAGGAGTTG AAGATAGATTTAATGCTTCATTAGGCGCCTACCATGATTTGCTAAAAATT ATTAAAGATAAAGATTTTTTGGATAATGAAGAAAATGAAGATATCTTAGA GGATATTGTTTTAACATTGACCTTATTTGAAGATAGGGGGATGATTGAGG AAAGACTTAAAACATATGCTCACCTCTTTGATGATAAGGTGATGAAACAG CTTAAACGTCGCCGTTATACTGGTTGGGGACGTTTGTCTCGAAAATTGAT TAATGGTATTAGGGATAAGCAATCTGGCAAAACAATATTAGATTTTTTGA AATCAGATGGTTTTGCCAATCGCAATTTTATGCAGCTGATCCATGATGAT AGTTTGACATTTAAAGAAGATATTCAAAAAGCACAGGTGTCTGGACAAGG CCATAGTTTACATGAACAGATTGCTAACTTAGCTGGCAGTCCTGCTATTA AAAAAGGTATTTTACAGACTGTAAAAATTGTTGATGAACTGGTCAAAGTA ATGGGGCATAAGCCAGAAAATATCGTTATTGAAATGGCACGTGAAAATCA GACAACTCAAAAGGGCCAGAAAAATTCGCGAGAGCGTATGAAACGAATCG AAGAAGGTATCAAAGAATTAGGAAGTCAGATTCTTAAAGAGCATCCTGTT GAAAATACTCAATTGCAAAATGAAAAGCTCTATCTCTATTATCTACAAAA TGGAAGAGACATGTATGTGGACCAAGAATTAGATATTAATCGTTTAAGTG ATTATGATGTCGATCACATTGTTCCACAAAGTTTCATTAAAGACGATTCA ATAGACAATAAGGTACTAACGCGTTCTGATAAAAATCGTGGTAAATCGGA TAACGTTCCAAGTGAAGAAGTAGTCAAAAAGATGAAAAACTATTGGAGAC AACTTCTAAACGCCAAGTTAATCACTCAACGTAAGTTTGATAATTTAACG AAAGCTGAACGTGGAGGTTTGAGTGAACTTGATAAAGCTGGTTTTATCAA ACGCCAATTGGTTGAAACTCGCCAAATCACTAAGCATGTGGCACAAATTT TGGATAGTCGCATGAATACTAAATACGATGAAAATGATAAACTTATTCGA GAGGTTAAAGTGATTACCTTAAAATCTAAATTAGTTTCTGACTTCCGAAA AGATTTCCAATTCTATAAAGTACGTGAGATTAACAATTACCATCATGCCC ATGATGCGTATCTAAATGCCGTCGTTGGAACTGCTTTGATTAAGAAATAT CCAAAACTTGAATCGGAGTTTGTCTATGGTGATTATAAAGTTTATGATGT TCGTAAAATGATTGCTAAGTCTGAGCAAGAAATAGGCAAAGCAACCGCAA AATATTTCTTTTACTCTAATATCATGAACTTCTTCAAAACAGAAATTACA CTTGCAAATGGAGAGATTCGCAAACGCCCTCTAATCGAAACTAATGGGGA AACTGGAGAAATTGTCTGGGATAAAGGGCGAGATTTTGCCACAGTGCGCA AAGTATTGTCCATGCCCCAAGTCAATATTGTCAAGAAAACAGAAGTACAG ACAGGCGGATTCTCCAAGGAGTCAATTTTACCAAAAAGAAATTCGGACAA GCTTATTGCTCGTAAAAAAGACTGGGATCCAAAAAAATATGGTGGTTTTG ATAGTCCAACGGTAGCTTATTCAGTCCTAGTGGTTGCTAAGGTGGAAAAA GGGAAATCGAAGAAGTTAAAATCCGTTAAAGAGTTACTAGGGATCACAAT TATGGAAAGAAGTTCCTTTGAAAAAAATCCGATTGACTTTTTAGAAGCTA AAGGATATAAGGAAGTTAAAAAAGACTTAATCATTAAACTACCTAAATAT AGTCTTTTTGAGTTAGAAAACGGTCGTAAACGGATGCTGGCTAGTGCCGG AGAATTACAAAAAGGAAATGAGCTGGCTCTGCCAAGCAAATATGTGAATT TTTTATATTTAGCTAGTCATTATGAAAAGTTGAAGGGTAGTCCAGAAGAT AACGAACAAAAACAATTGTTTGTGGAGCAGCATAAGCATTATTTAGATGA GATTATTGAGCAAATCAGTGAATTTTCTAAGCGTGTTATTTTAGCAGATG CCAATTTAGATAAAGTTCTTAGTGCATATAACAAACATAGAGACAAACCA ATACGTGAACAAGCAGAAAATATTATTCATTTATTTACGTTGACGAATCT TGGAGCTCCCGCTGCTTTTAAATATTTTGATACAACAATTGATCGTAAAC GATATACGTCTACAAAAGAAGTTTTAGATGCCACTCTTATCCATCAATCC ATCACTGGTCTTTATGAAACACGCATTGATTTGAGTCAGCTAGGAGGTGA CTGA (SEQ ID NO: 41) MDKKYSIGLDIGTNSVGWAVITDDYKVPSKKFKVLGNTDRHSIKKNLIGA LLFGSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHR LEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLADSTDKAD LRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQIYNQLFEENP INASRVDAKAILSARLSKSRRLENLIAQLPGEKRNGLFGNLIALSLGLTP NFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAI LLSDILRVNSEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEI FFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLR KQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPY YVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDK NLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVD LLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGAYHDLLKI IKDKDFLDNEENEDILEDIVLTLTLFEDRGMIEERLKTYAHLFDDKVMKQ LKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDD SLTFKEDIQKAQVSGQGHSLHEQIANLAGSPAIKKGILQTVKIVDELVKV MGHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPV ENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSFIKDDS IDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLT KAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIR EVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKY PKLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEIT LANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQ TGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEK GKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKY SLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPED NEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKP IREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQS ITGLYETRIDLSQLGGD

The term “concatemer,” as used herein in the context of nucleic acid molecules, refers to a nucleic acid molecule that contains multiple copies of the same DNA sequences linked in a series. For example, a concatemer comprising ten copies of a specific sequence of nucleotides (e.g., [XYZ]₁₀), would comprise ten copies of the same specific sequence linked to each other in series, e.g., 5′-XYZXYZXYZXYZXYZXYZXYZXYZXYZXYZ-3′. A concatemer may comprise any number of copies of the repeat unit or sequence, e.g., at least 2 copies, at least 3 copies, at least 4 copies, at least 5 copies, at least 10 copies, at least 100 copies, at least 1000 copies, etc. An example of a concatemer of a nucleic acid sequence comprising a nuclease target site and a constant insert sequence would be [(target site)-(constant insert sequence)]₃₀₀. A concatemer may be a linear nucleic acid molecule, or may be circular.

The terms “conjugating,” “conjugated,” and “conjugation” refer to an association of two entities, for example, of two molecules such as two proteins, two domains (e.g., a binding domain and a cleavage domain), or a protein and an agent, e.g., a protein binding domain and a small molecule. In some aspects, the association is between a protein (e.g., RNA-programmable nuclease) and a nucleic acid (e.g., a guide RNA). The association can be, for example, via a direct or indirect (e.g., via a linker) covalent linkage or via non-covalent interactions. In some embodiments, the association is covalent. In some embodiments, two molecules are conjugated via a linker connecting both molecules. For example, in some embodiments where two proteins are conjugated to each other, e.g., a binding domain and a cleavage domain of an engineered nuclease, to form a protein fusion, the two proteins may be conjugated via a polypeptide linker, e.g., an amino acid sequence connecting the C-terminus of one protein to the N-terminus of the other protein.

The term “consensus sequence,” as used herein in the context of nucleic acid sequences, refers to a calculated sequence representing the most frequent nucleotide residues found at each position in a plurality of similar sequences. Typically, a consensus sequence is determined by sequence alignment in which similar sequences are compared to each other and similar sequence motifs are calculated. In the context of nuclease target site sequences, a consensus sequence of a nuclease target site may, in some embodiments, be the sequence most frequently bound, or bound with the highest affinity, by a given nuclease. With respect to RNA-programmable nuclease (e.g., Cas9) target site sequences, the consensus sequence may, in some embodiments, be the sequence or region to which a gRNA, or a plurality of gRNAs, is expected or designed to bind, e.g., based on complementary base pairing.

The term “effective amount,” as used herein, refers to an amount of a biologically active agent that is sufficient to elicit a desired biological response. For example, in some embodiments, an effective amount of a nuclease may refer to the amount of the nuclease that is sufficient to induce cleavage of a target site specifically bound and cleaved by the nuclease. As will be appreciated by the skilled artisan, the effective amount of an agent, e.g., a nuclease, a hybrid protein, or a polynucleotide, may vary depending on various factors as, for example, on the desired biological response, the specific allele, genome, target site, cell, or tissue being targeted, and the agent being used.

The term “enediyne,” as used herein, refers to a class of bacterial natural products characterized by either nine- and ten-membered rings containing two triple bonds separated by a double bond (see, e.g., K. C. Nicolaou; A. L. Smith; E. W. Yue (1993). “Chemistry and biology of natural and designed enediynes”. PNAS 90 (13): 5881-5888; the entire contents of which are incorporated herein by reference). Some enediynes are capable of undergoing Bergman cyclization, and the resulting diradical, a 1,4-dehydrobenzene derivative, is capable of abstracting hydrogen atoms from the sugar backbone of DNA which results in DNA strand cleavage (see, e.g., S. Walker; R. Landovitz; W. D. Ding; G. A. Ellestad; D. Kahne (1992). “Cleavage behavior of calicheamicin gamma 1 and calicheamicin T”. Proc Natl Acad Sci U.S.A. 89 (10): 4608-12; the entire contents of which are incorporated herein by reference). Their reactivity with DNA confers an antibiotic character to many enediynes, and some enediynes are clinically investigated as anticancer antibiotics. Nonlimiting examples of enediynes are dynemicin, neocarzinostatin, calicheamicin, esperamicin (see, e.g., Adrian L. Smith and K. C. Bicolaou, “The Enediyne Antibiotics” J. Med. Chem., 1996, 39 (11), pp 2103-2117; and Donald Borders, “Enediyne antibiotics as antitumor agents,” Informa Healthcare; 1^(st) edition (Nov. 23, 1994, ISBN-10: 0824789385; the entire contents of which are incorporated herein by reference).

The term “homing endonuclease,” as used herein, refers to a type of restriction enzymes typically encoded by introns or inteins Edgell D R (February 2009). “Selfish DNA: homing endonucleases find a home”. Curr Biol 19 (3): R115-R117; Jasin M (June 1996). “Genetic manipulation of genomes with rare-cutting endonucleases”. Trends Genet 12 (6): 224-8; Burt A, Koufopanou V (December 2004). “Homing endonuclease genes: the rise and fall and rise again of a selfish element”. Curr Opin Genet Dev 14 (6): 609-15; the entire contents of which are incorporated herein by reference. Homing endonuclease recognition sequences are long enough to occur randomly only with a very low probability (approximately once every 7×10¹⁰ bp), and are normally found in only one instance per genome.

The term “library,” as used herein in the context of nucleic acids or proteins, refers to a population of two or more different nucleic acids or proteins, respectively. For example, a library of nuclease target sites comprises at least two nucleic acid molecules comprising different nuclease target sites. In some embodiments, a library comprises at least 10¹, at least 10², at least 10³, at least 10⁴, at least 10⁵, at least 10⁶, at least 10⁷, at least 10⁸, at least 10⁹, at least 10¹⁰, at least 10¹¹, at least 10¹², at least 10¹³, at least 10¹⁴, or at least 10¹⁵ different nucleic acids or proteins. In some embodiments, the members of the library may comprise randomized sequences, for example, fully or partially randomized sequences. In some embodiments, the library comprises nucleic acid molecules that are unrelated to each other, e.g., nucleic acids comprising fully randomized sequences. In other embodiments, at least some members of the library may be related, for example, they may be variants or derivatives of a particular sequence, such as a consensus target site sequence.

The term “linker,” as used herein, refers to a chemical group or a molecule linking two adjacent molecules or moieties, e.g., a binding domain and a cleavage domain of a nuclease. Typically, the linker is positioned between, or flanked by, two groups, molecules, or other moieties and connected to each one via a covalent bond, thus connecting the two. In some embodiments, the linker is an amino acid or a plurality of amino acids (e.g., a peptide or protein). In some embodiments, the linker is an organic molecule, group, polymer, or chemical moiety.

The term “nuclease,” as used herein, refers to an agent, for example a protein or a small molecule, capable of cleaving a phosphodiester bond connecting nucleotide residues in a nucleic acid molecule. In some embodiments, a nuclease is a protein, e.g., an enzyme that can bind a nucleic acid molecule and cleave a phosphodiester bond connecting nucleotide residues within the nucleic acid molecule. A nuclease may be an endonuclease, cleaving a phosphodiester bonds within a polynucleotide chain, or an exonuclease, cleaving a phosphodiester bond at the end of the polynucleotide chain. In some embodiments, a nuclease is a site-specific nuclease, binding and/or cleaving a specific phosphodiester bond within a specific nucleotide sequence, which is also referred to herein as the “recognition sequence,” the “nuclease target site,” or the “target site.” In some embodiments, a nuclease is a RNA-guided (i.e., RNA-programmable) nuclease, which complexes with (e.g., binds with) an RNA having a sequence that complements a target site, thereby providing the sequence specificity of the nuclease. In some embodiments, a nuclease recognizes a single stranded target site, while in other embodiments, a nuclease recognizes a double-stranded target site, for example a double-stranded DNA target site. The target sites of many naturally occurring nucleases, for example, many naturally occurring DNA restriction nucleases, are well known to those of skill in the art. In many cases, a DNA nuclease, such as EcoRI, HindIII, or BamHI, recognize a palindromic, double-stranded DNA target site of 4 to 10 base pairs in length, and cut each of the two DNA strands at a specific position within the target site. Some endonucleases cut a double-stranded nucleic acid target site symmetrically, i.e., cutting both strands at the same position so that the ends comprise base-paired nucleotides, also referred to herein as blunt ends. Other endonucleases cut a double-stranded nucleic acid target sites asymmetrically, i.e., cutting each strand at a different position so that the ends comprise unpaired nucleotides. Unpaired nucleotides at the end of a double-stranded DNA molecule are also referred to as “overhangs,” e.g., as “5′-overhang” or as “3′-overhang,” depending on whether the unpaired nucleotide(s) form(s) the 5′ or the 3′ end of the respective DNA strand. Double-stranded DNA molecule ends ending with unpaired nucleotide(s) are also referred to as sticky ends, as they can “stick to” other double-stranded DNA molecule ends comprising complementary unpaired nucleotide(s). A nuclease protein typically comprises a “binding domain” that mediates the interaction of the protein with the nucleic acid substrate, and also, in some cases, specifically binds to a target site, and a “cleavage domain” that catalyzes the cleavage of the phosphodiester bond within the nucleic acid backbone. In some embodiments a nuclease protein can bind and cleave a nucleic acid molecule in a monomeric form, while, in other embodiments, a nuclease protein has to dimerize or multimerize in order to cleave a target nucleic acid molecule. Binding domains and cleavage domains of naturally occurring nucleases, as well as modular binding domains and cleavage domains that can be fused to create nucleases binding specific target sites, are well known to those of skill in the art. For example, zinc fingers or transcriptional activator like elements can be used as binding domains to specifically bind a desired target site, and fused or conjugated to a cleavage domain, for example, the cleavage domain of FokI, to create an engineered nuclease cleaving the target site.

The terms “nucleic acid” and “nucleic acid molecule,” as used herein, refer to a compound comprising a nucleobase and an acidic moiety, e.g., a nucleoside, a nucleotide, or a polymer of nucleotides. Typically, polymeric nucleic acids, e.g., nucleic acid molecules comprising three or more nucleotides are linear molecules, in which adjacent nucleotides are linked to each other via a phosphodiester linkage. In some embodiments, “nucleic acid” refers to individual nucleic acid residues (e.g. nucleotides and/or nucleosides). In some embodiments, “nucleic acid” refers to an oligonucleotide chain comprising three or more individual nucleotide residues. As used herein, the terms “oligonucleotide” and “polynucleotide” can be used interchangeably to refer to a polymer of nucleotides (e.g., a string of at least three nucleotides). In some embodiments, “nucleic acid” encompasses RNA as well as single and/or double-stranded DNA. Nucleic acids may be naturally occurring, for example, in the context of a genome, a transcript, an mRNA, tRNA, rRNA, siRNA, snRNA, a plasmid, cosmid, chromosome, chromatid, or other naturally occurring nucleic acid molecule. On the other hand, a nucleic acid molecule may be a non-naturally occurring molecule, e.g., a recombinant DNA or RNA, an artificial chromosome, an engineered genome, or fragment thereof, or a synthetic DNA, RNA, DNA/RNA hybrid, or including non-naturally occurring nucleotides or nucleosides. Furthermore, the terms “nucleic acid,” “DNA,” “RNA,” and/or similar terms include nucleic acid analogs, i.e. analogs having other than a phosphodiester backbone. Nucleic acids can be purified from natural sources, produced using recombinant expression systems and optionally purified, chemically synthesized, etc. Where appropriate, e.g., in the case of chemically synthesized molecules, nucleic acids can comprise nucleoside analogs such as analogs having chemically modified bases or sugars, and backbone modifications. A nucleic acid sequence is presented in the 5′ to 3′ direction unless otherwise indicated. In some embodiments, a nucleic acid is or comprises natural nucleosides (e.g. adenosine, thymidine, guanosine, cytidine, uridine, deoxyadenosine, deoxythymidine, deoxyguanosine, and deoxycytidine); nucleoside analogs (e.g., 2-aminoadenosine, 2-thiothymidine, inosine, pyrrolo-pyrimidine, 3-methyl adenosine, 5-methylcytidine, 2-aminoadenosine, C5-bromouridine, C5-fluorouridine, C5-iodouridine, C5-propynyl-uridine, C5-propynyl-cytidine, C5-methylcytidine, 2-aminoadenosine, 7-deazaadenosine, 7-deazaguanosine, 8-oxoadenosine, 8-oxoguanosine, O(6)-methylguanine, and 2-thiocytidine); chemically modified bases; biologically modified bases (e.g., methylated bases); intercalated bases; modified sugars (e.g., 2′-fluororibose, ribose, 2′-deoxyribose, arabinose, and hexose); and/or modified phosphate groups (e.g., phosphorothioates and 5′-N-phosphoramidite linkages).

The term “pharmaceutical composition,” as used herein, refers to a composition that can be administrated to a subject in the context of treatment of a disease or disorder. In some embodiments, a pharmaceutical composition comprises an active ingredient, e.g., a nuclease or a nucleic acid encoding a nuclease, and a pharmaceutically acceptable excipient.

The term “proliferative disease,” as used herein, refers to any disease in which cell or tissue homeostasis is disturbed in that a cell or cell population exhibits an abnormally elevated proliferation rate. Proliferative diseases include hyperproliferative diseases, such as pre-neoplastic hyperplastic conditions and neoplastic diseases. Neoplastic diseases are characterized by an abnormal proliferation of cells and include both benign and malignant neoplasias. Malignant neoplasia is also referred to as cancer.

The terms “protein,” “peptide,” and “polypeptide” are used interchangeably herein, and refer to a polymer of amino acid residues linked together by peptide (amide) bonds. The terms refer to a protein, peptide, or polypeptide of any size, structure, or function. Typically, a protein, peptide, or polypeptide will be at least three amino acids long. A protein, peptide, or polypeptide may refer to an individual protein or a collection of proteins. One or more of the amino acids in a protein, peptide, or polypeptide may be modified, for example, by the addition of a chemical entity such as a carbohydrate group, a hydroxyl group, a phosphate group, a farnesyl group, an isofarnesyl group, a fatty acid group, a linker for conjugation, functionalization, or other modification, etc. A protein, peptide, or polypeptide may also be a single molecule or may be a multi-molecular complex. A protein, peptide, or polypeptide may be just a fragment of a naturally occurring protein or peptide. A protein, peptide, or polypeptide may be naturally occurring, recombinant, or synthetic, or any combination thereof. A protein may comprise different domains, for example, a nucleic acid binding domain and a nucleic acid cleavage domain. In some embodiments, a protein comprises a proteinaceous part, e.g., an amino acid sequence constituting a nucleic acid binding domain, and an organic compound, e.g., a compound that can act as a nucleic acid cleavage agent. In some embodiments, a protein is in a complex with, or is in association with, a nucleic acid, e.g., RNA.

The term “randomized,” as used herein in the context of nucleic acid sequences, refers to a sequence or residue within a sequence that has been synthesized to incorporate a mixture of free nucleotides, for example, a mixture of all four nucleotides A, T, G, and C. Randomized residues are typically represented by the letter N within a nucleotide sequence. In some embodiments, a randomized sequence or residue is fully randomized, in which case the randomized residues are synthesized by adding equal amounts of the nucleotides to be incorporated (e.g., 25% T, 25% A, 25% G, and 25% C) during the synthesis step of the respective sequence residue. In some embodiments, a randomized sequence or residue is partially randomized, in which case the randomized residues are synthesized by adding non-equal amounts of the nucleotides to be incorporated (e.g., 79% T, 7% A, 7% G, and 7% C) during the synthesis step of the respective sequence residue. Partial randomization allows for the generation of sequences that are templated on a given sequence, but have incorporated mutations at a desired frequency. For example, if a known nuclease target site is used as a synthesis template, partial randomization in which at each step the nucleotide represented at the respective residue is added to the synthesis at 79%, and the other three nucleotides are added at 7% each, will result in a mixture of partially randomized target sites being synthesized, which still represent the consensus sequence of the original target site, but which differ from the original target site at each residue with a statistical frequency of 21% for each residue so synthesized (distributed binomially). In some embodiments, a partially randomized sequence differs from the consensus sequence by more than 5%, more than 10%, more than 15%, more than 20%, more than 25%, or more than 30% on average, distributed binomially. In some embodiments, a partially randomized sequence differs from the consensus site by no more than 10%, no more than 15%, no more than 20%, no more than 25%, nor more than 30%, no more than 40%, or no more than 50% on average, distributed binomially.

The term “RNA-programmable nuclease,” and “RNA-guided nuclease” are used interchangeably herein and refer to a nuclease that forms a complex with (e.g., binds or associates with) one or more RNA that is not a target for cleavage. In some embodiments, an RNA-programmable nuclease, when in a complex with an RNA, may be referred to as a nuclease:RNA complex. Typically, the bound RNA(s) is referred to as a guide RNA (gRNA) or a single-guide RNA (sgRNA). The gRNA/sgRNA comprises a nucleotide sequence that complements a target site, which mediates binding of the nuclease/RNA complex to said target site and providing the sequence specificity of the nuclease:RNA complex. In some embodiments, the RNA-programmable nuclease is the (CRISPR-associated system) Cas9 endonuclease, for example Cas9 (Csn1) from Streptococcus pyogenes (see, e.g., “Complete genome sequence of an M1 strain of Streptococcus pyogenes.” Ferretti J. J., McShan W. M., Ajdic D. J., Savic D. J., Savic G., Lyon K., Primeaux C., Sezate S., Suvorov A. N., Kenton S., Lai H. S., Lin S. P., Qian Y., Jia H. G., Najar F. Z., Ren Q., Zhu H., Song L. expand/collapse author list McLaughlin R. E., Proc. Natl. Acad. Sci. U.S.A. 98:4658-4663(2001); “CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III.” Deltcheva E., Chylinski K., Sharma C. M., Gonzales K., Chao Y., Pirzada Z. A., Eckert M. R., Vogel J., Charpentier E., Nature 471:602-607(2011); and “A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.” Jinek M., Chylinski K., Fonfara I., Hauer M., Doudna J. A., Charpentier E. Science 337:816-821(2012), the entire contents of each of which are incorporated herein by reference

Because RNA-programmable nucleases (e.g., Cas9) use RNA:DNA hybridization to determine target DNA cleavage sites, these proteins are able to cleave, in principle, any sequence specified by the guide RNA. Methods of using RNA-programmable nucleases, such as Cas9, for site-specific cleavage (e.g., to modify a genome) are known in the art (See e.g., Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819-823 (2013); Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 823-826 (2013); Hwang, W. Y. et al. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nature biotechnology 31, 227-229 (2013); Jinek, M. et al. RNA-programmed genome editing in human cells. eLife 2, e00471 (2013); Dicarlo, J. E. et al. Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic acids research (2013); Jiang, W. et al. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nature biotechnology 31, 233-239 (2013); the entire contents of each of which are incorporated herein by reference).

The terms “small molecule” and “organic compound” are used interchangeably herein and refer to molecules, whether naturally-occurring or artificially created (e.g., via chemical synthesis) that have a relatively low molecular weight. Typically, an organic compound contains carbon. An organic compound may contain multiple carbon-carbon bonds, stereocenters, and other functional groups (e.g., amines, hydroxyl, carbonyls, or heterocyclic rings). In some embodiments, organic compounds are monomeric and have a molecular weight of less than about 1500 g/mol. In certain embodiments, the molecular weight of the small molecule is less than about 1000 g/mol or less than about 500 g/mol. In certain embodiments, the small molecule is a drug, for example, a drug that has already been deemed safe and effective for use in humans or animals by the appropriate governmental agency or regulatory body. In certain embodiments, the organic molecule is known to bind and/or cleave a nucleic acid. In some embodiments, the organic compound is an enediyne. In some embodiments, the organic compound is an antibiotic drug, for example, an anticancer antibiotic such as dynemicin, neocarzinostatin, calicheamicin, esperamicin, bleomycin, or a derivative thereof.

The term “subject,” as used herein, refers to an individual organism, for example, an individual mammal. In some embodiments, the subject is a human. In some embodiments, the subject is a non-human mammal In some embodiments, the subject is a non-human primate. In some embodiments, the subject is a rodent. In some embodiments, the subject is a sheep, a goat, a cattle, a cat, or a dog. In some embodiments, the subject is a vertebrate, an amphibian, a reptile, a fish, an insect, a fly, or a nematode.

The terms “target nucleic acid,” and “target genome,” as used herein in the context of nucleases, refer to a nucleic acid molecule or a genome, respectively, that comprises at least one target site of a given nuclease.

The term “target site,” used herein interchangeably with the term “nuclease target site,” refers to a sequence within a nucleic acid molecule that is bound and cleaved by a nuclease. A target site may be single-stranded or double-stranded. In the context of nucleases that dimerize, for example, nucleases comprising a FokI DNA cleavage domain, a target sites typically comprises a left-half site (bound by one monomer of the nuclease), a right-half site (bound by the second monomer of the nuclease), and a spacer sequence between the half sites in which the cut is made. This structure ([left-half site]-[spacer sequence]-[right-half site]) is referred to herein as an LSR structure. In some embodiments, the left-half site and/or the right-half site is between 10-18 nucleotides long. In some embodiments, either or both half-sites are shorter or longer. In some embodiments, the left and right half sites comprise different nucleic acid sequences. In the context of zinc finger nucleases, target sites may, in some embodiments comprise two half-sites that are each 6-18 bp long flanking a non-specified spacer region that is 4-8 bp long. In the context of TALENs, target sites may, in some embodiments, comprise two half-sites sites that are each 10-23 bp long flanking a non-specified spacer region that is 10-30 bp long. In the context of RNA-guided (e.g., RNA-programmable) nucleases, a target site typically comprises a nucleotide sequence that is complementary to the sgRNA of the RNA-programmable nuclease, and a protospacer adjacent motif (PAM) at the 3′ end adjacent to the sgRNA-complementary sequence. For the RNA-guided nuclease Cas9, the target site may be, in some embodiments, 20 base pairs plus a 3 base pair PAM (e.g., NNN, wherein N represents any nucleotide). Typically, the first nucleotide of a PAM can be any nucleotide, while the two downstream nucleotides are specified depending on the specific RNA-guided nuclease. Exemplary target sites for RNA-guided nucleases, such as Cas9, are known to those of skill in the art and include, without limitation, NNG, NGN, NAG, and NGG, wherein N represents any nucleotide. In addition, Cas9 nucleases from different species (e.g., S. thermophilus instead of S. pyogenes) recognizes a PAM that comprises the sequence NGGNG. Additional PAM sequences are known, including, but not limited to NNAGAAW and NAAR (see, e.g., Esvelt and Wang, Molecular Systems Biology, 9:641 (2013), the entire contents of which are incorporated herein by reference). For example, the target site of an RNA-guided nuclease, such as, e.g., Cas9, may comprise the structure [N_(Z)]-[PAM], where each N is, independently, any nucleotide, and _(Z) is an integer between 1 and 50. In some embodiments, _(Z) is at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50. In some embodiments, _(Z) is 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48,49, or 50. In some embodiments, Z is 20.

The term “Transcriptional Activator-Like Effector,” (TALE) as used herein, refers to bacterial proteins comprising a DNA binding domain, which contains a highly conserved 33-34 amino acid sequence comprising a highly variable two-amino acid motif (Repeat Variable Diresidue, RVD). The RVD motif determines binding specificity to a nucleic acid sequence, and can be engineered according to methods well known to those of skill in the art to specifically bind a desired DNA sequence (see, e.g., Miller, Jeffrey; et. al. (February 2011). “A TALE nuclease architecture for efficient genome editing”. Nature Biotechnology 29 (2): 143-8; Zhang, Feng; et. al. (February 2011). “Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription”. Nature Biotechnology 29 (2): 149-53; Geiβler, R.; Scholze, H.; Hahn, S.; Streubel, J.; Bonas, U.; Behrens, S. E.; Boch, J. (2011), Shiu, Shin-Han. ed. “Transcriptional Activators of Human Genes with Programmable DNA-Specificity”. PLoS ONE 6 (5): e19509; Boch, Jens (February 2011). “TALEs of genome targeting”. Nature Biotechnology 29 (2): 135-6; Boch, Jens; et. al. (December 2009). “Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors”. Science 326 (5959): 1509-12; and Moscou, Matthew J.; Adam J. Bogdanove (December 2009). “A Simple Cipher Governs DNA Recognition by TAL Effectors”. Science 326 (5959): 1501; the entire contents of each of which are incorporated herein by reference). The simple relationship between amino acid sequence and DNA recognition has allowed for the engineering of specific DNA binding domains by selecting a combination of repeat segments containing the appropriate RVDs.

The term “Transcriptional Activator-Like Element Nuclease,” (TALEN) as used herein, refers to an artificial nuclease comprising a transcriptional activator like effector DNA binding domain to a DNA cleavage domain, for example, a FokI domain. A number of modular assembly schemes for generating engineered TALE constructs have been reported (see e.g., Zhang, Feng; et. al. (February 2011). “Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription”. Nature Biotechnology 29 (2): 149-53; Geiβler, R.; Scholze, H.; Hahn, S.; Streubel, J.; Bonas, U.; Behrens, S. E.; Boch, J. (2011), Shiu, Shin-Han. ed. “Transcriptional Activators of Human Genes with Programmable DNA-Specificity”. PLoS ONE 6 (5): e19509; Cermak, T.; Doyle, E. L.; Christian, M.; Wang, L.; Zhang, Y.; Schmidt, C.; Bailer, J. A.; Somia, N. V. et al. (2011). “Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting”. Nucleic Acids Research; Morbitzer, R.; Elsaesser, J.; Hausner, J.; Lahaye, T. (2011). “Assembly of custom TALE-type DNA binding domains by modular cloning”. Nucleic Acids Research; Li, T.; Huang, S.; Zhao, X.; Wright, D. A.; Carpenter, S.; Spalding, M. H.; Weeks, D. P.; Yang, B. (2011). “Modularly assembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes”. Nucleic Acids Research.; Weber, E.; Gruetzner, R.; Werner, S.; Engler, C.; Marillonnet, S. (2011). Bendahmane, Mohammed. ed. “Assembly of Designer TAL Effectors by Golden Gate Cloning”. PLoS ONE 6 (5): e19722; the entire contents of each of which are incorporated herein by reference).

The terms “treatment,” “treat,” and “treating,” refer to a clinical intervention aimed to reverse, alleviate, delay the onset of, or inhibit the progress of a disease or disorder, or one or more symptoms thereof, as described herein. As used herein, the terms “treatment,” “treat,” and “treating” refer to a clinical intervention aimed to reverse, alleviate, delay the onset of, or inhibit the progress of a disease or disorder, or one or more symptoms thereof, as described herein. In some embodiments, treatment may be administered after one or more symptoms have developed and/or after a disease has been diagnosed. In other embodiments, treatment may be administered in the absence of symptoms, e.g., to prevent or delay onset of a symptom or inhibit onset or progression of a disease. For example, treatment may be administered to a susceptible individual prior to the onset of symptoms (e.g., in light of a history of symptoms and/or in light of genetic or other susceptibility factors). Treatment may also be continued after symptoms have resolved, for example to prevent or delay their recurrence.

The term “zinc finger,” as used herein, refers to a small nucleic acid-binding protein structural motif characterized by a fold and the coordination of one or more zinc ions that stabilize the fold. Zinc fingers encompass a wide variety of differing protein structures (see, e.g., Klug A, Rhodes D (1987). “Zinc fingers: a novel protein fold for nucleic acid recognition”. Cold Spring Harb. Symp. Quant. Biol. 52: 473-82, the entire contents of which are incorporated herein by reference). Zinc fingers can be designed to bind a specific sequence of nucleotides, and zinc finger arrays comprising fusions of a series of zinc fingers, can be designed to bind virtually any desired target sequence. Such zinc finger arrays can form a binding domain of a protein, for example, of a nuclease, e.g., if conjugated to a nucleic acid cleavage domain. Different type of zinc finger motifs are known to those of skill in the art, including, but not limited to, Cys₂His₂, Gag knuckle, Treble clef, Zinc ribbon, Zn₂/Cys₆, and TAZ2 domain-like motifs (see, e.g., Krishna S S, Majumdar I, Grishin N V (January 2003). “Structural classification of zinc fingers: survey and summary”. Nucleic Acids Res. 31 (2): 532-50). Typically, a single zinc finger motif binds 3 or 4 nucleotides of a nucleic acid molecule. Accordingly, a zinc finger domain comprising 2 zinc finger motifs may bind 6-8 nucleotides, a zinc finger domain comprising 3 zinc finger motifs may bind 9-12 nucleotides, a zinc finger domain comprising 4 zinc finger motifs may bind 12-16 nucleotides, and so forth. Any suitable protein engineering technique can be employed to alter the DNA-binding specificity of zinc fingers and/or design novel zinc finger fusions to bind virtually any desired target sequence from 3-30 nucleotides in length (see, e.g., Pabo C O, Peisach E, Grant R A (2001). “Design and selection of novel cys2His2 Zinc finger proteins”. Annual Review of Biochemistry 70: 313-340; Jamieson A C, Miller J C, Pabo C O (2003). “Drug discovery with engineered zinc-finger proteins”. Nature Reviews Drug Discovery 2 (5): 361-368; and Liu Q, Segal D J, Ghiara J B, Barbas C F (May 1997). “Design of polydactyl zinc-finger proteins for unique addressing within complex genomes”. Proc. Natl. Acad. Sci. U.S.A. 94 (11); the entire contents of each of which are incorporated herein by reference). Fusions between engineered zinc finger arrays and protein domains that cleave a nucleic acid can be used to generate a “zinc finger nuclease.” A zinc finger nuclease typically comprises a zinc finger domain that binds a specific target site within a nucleic acid molecule, and a nucleic acid cleavage domain that cuts the nucleic acid molecule within or in proximity to the target site bound by the binding domain. Typical engineered zinc finger nucleases comprise a binding domain having between 3 and 6 individual zinc finger motifs and binding target sites ranging from 9 base pairs to 18 base pairs in length. Longer target sites are particularly attractive in situations where it is desired to bind and cleave a target site that is unique in a given genome.

The term “zinc finger nuclease,” as used herein, refers to a nuclease comprising a nucleic acid cleavage domain conjugated to a binding domain that comprises a zinc finger array. In some embodiments, the cleavage domain is the cleavage domain of the type II restriction endonuclease FokI. Zinc finger nucleases can be designed to target virtually any desired sequence in a given nucleic acid molecule for cleavage, and the possibility to the design zinc finger binding domains to bind unique sites in the context of complex genomes allows for targeted cleavage of a single genomic site in living cells, for example, to achieve a targeted genomic alteration of therapeutic value. Targeting a double-strand break to a desired genomic locus can be used to introduce frame-shift mutations into the coding sequence of a gene due to the error-prone nature of the non-homologous DNA repair pathway. Zinc finger nucleases can be generated to target a site of interest by methods well known to those of skill in the art. For example, zinc finger binding domains with a desired specificity can be designed by combining individual zinc finger motifs of known specificity. The structure of the zinc finger protein Zif268 bound to DNA has informed much of the work in this field and the concept of obtaining zinc fingers for each of the 64 possible base pair triplets and then mixing and matching these modular zinc fingers to design proteins with any desired sequence specificity has been described (Pavletich N P, Pabo C O (May 1991). “Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A”. Science 252 (5007): 809-17, the entire contents of which are incorporated herein). In some embodiments, separate zinc fingers that each recognize a 3 base pair DNA sequence are combined to generate 3-, 4-, 5-, or 6-finger arrays that recognize target sites ranging from 9 base pairs to 18 base pairs in length. In some embodiments, longer arrays are contemplated. In other embodiments, 2-finger modules recognizing 6-8 nucleotides are combined to generate 4-, 6-, or 8-zinc finger arrays. In some embodiments, bacterial or phage display is employed to develop a zinc finger domain that recognizes a desired nucleic acid sequence, for example, a desired nuclease target site of 3-30 bp in length. Zinc finger nucleases, in some embodiments, comprise a zinc finger binding domain and a cleavage domain fused or otherwise conjugated to each other via a linker, for example, a polypeptide linker. The length of the linker determines the distance of the cut from the nucleic acid sequence bound by the zinc finger domain. If a shorter linker is used, the cleavage domain will cut the nucleic acid closer to the bound nucleic acid sequence, while a longer linker will result in a greater distance between the cut and the bound nucleic acid sequence. In some embodiments, the cleavage domain of a zinc finger nuclease has to dimerize in order to cut a bound nucleic acid. In some such embodiments, the dimer is a heterodimer of two monomers, each of which comprise a different zinc finger binding domain. For example, in some embodiments, the dimer may comprise one monomer comprising zinc finger domain A conjugated to a FokI cleavage domain, and one monomer comprising zinc finger domain B conjugated to a FokI cleavage domain. In this nonlimiting example, zinc finger domain A binds a nucleic acid sequence on one side of the target site, zinc finger domain B binds a nucleic acid sequence on the other side of the target site, and the dimerize FokI domain cuts the nucleic acid in between the zinc finger domain binding sites.

DETAILED DESCRIPTION OF CERTAIN EMBODIMENTS OF THE INVENTION Introduction

Site-specific nucleases are powerful tools for targeted genome modification in vitro or in vivo. Some site specific nucleases can theoretically achieve a level of specificity for a target cleavage site that would allow one to target a single unique site in a genome for cleavage without affecting any other genomic site. It has been reported that nuclease cleavage in living cells triggers a DNA repair mechanism that frequently results in a modification of the cleaved, repaired genomic sequence, for example, via homologous recombination. Accordingly, the targeted cleavage of a specific unique sequence within a genome opens up new avenues for gene targeting and gene modification in living cells, including cells that are hard to manipulate with conventional gene targeting methods, such as many human somatic or embryonic stem cells. Nuclease-mediated modification of disease-related sequences, e.g., the CCR-5 allele in HIV/AIDS patients, or of genes necessary for tumor neovascularization, can be used in the clinical context, and two site specific nucleases are currently in clinical trials.

One important aspect in the field of site-specific nuclease-mediated modification are off-target nuclease effects, e.g., the cleavage of genomic sequences that differ from the intended target sequence by one or more nucleotides. Undesired side effects of off-target cleavage range from insertion into unwanted loci during a gene targeting event to severe complications in a clinical scenario. Off-target cleavage of sequences encoding essential gene functions or tumor suppressor genes by an endonuclease administered to a subject may result in disease or even death of the subject. Accordingly, it is desirable to characterize the cleavage preferences of a nuclease before using it in the laboratory or the clinic in order to determine its efficacy and safety. Further, the characterization of nuclease cleavage properties allows for the selection of the nuclease best suited for a specific task from a group of candidate nucleases, or for the selection of evolution products obtained from a plurality of nucleases. Such a characterization of nuclease cleavage properties may also inform the de-novo design of nucleases with enhanced properties, such as enhanced specificity or efficiency.

In many scenarios where a nuclease is employed for the targeted manipulation of a nucleic acid, cleavage specificity is a crucial feature. The imperfect specificity of some engineered nuclease binding domains can lead to off-target cleavage and undesired effects both in vitro and in vivo. Current methods of evaluating site-specific nuclease specificity, including ELISA assays, microarrays, one-hybrid systems, SELEX, and its variants, and Rosetta-based computational predictions, are all premised on the assumption that the binding specificity of the nuclease is equivalent or proportionate to their cleavage specificity.

It was previously discovered that the prediction of nuclease off-target binding effects constitute an imperfect approximation of a nuclease's off-target cleavage effects that may result in undesired biological effects (see PCT Application WO 2013/066438; and Pattanayak, V., Ramirez, C. L., Joung, J. K. & Liu, D. R. Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection. Nature methods 8, 765-770 (2011), the entire contents of each of which are incorporated herein by reference). This finding was consistent with the notion that the reported toxicity of some site specific DNA nucleases results from off-target DNA cleavage, rather than off-target binding alone.

The methods and reagents of the present disclosure represent, in some aspects, an improvement over previous methods and allow for an accurate evaluation of a given nuclease's target site specificity and provide strategies for the selection of suitable unique target sites and the design or selection of highly specific nucleases for the targeted cleavage of a single site in the context of a complex genome. For example, some previously reported methods for determining nuclease target site specificity profiles by screening libraries of nucleic acid molecules comprising candidate target sites relied on a “two-cut” in vitro selection method which requires indirect reconstruction of target sites from sequences of two half-sites resulting from two adjacent cuts of the nuclease of a library member nucleic acid (see e.g., Pattanayak, V. et al., Nature Methods 8, 765-770 (2011)). In contrast to such “two-cut” strategies, the methods of the present disclosure utilize a “one cut” screening strategy, which allows for the identification of library members that have been cut at least once by the nuclease. The “one-cut” selection strategies provided herein are compatible with single end high-throughput sequencing methods and do not require computational reconstruction of cleaved target sites from cut half-sites because they feature, in some embodiments, direct sequencing of an intact target nuclease sequence in a cut library member nucleic acid.

Additionally, the presently disclosed “one-cut” screening methods utilize concatemers of a candidate nuclease target site and constant insert region that are about 10-fold shorter than previously reported constructs used for two-cut strategies (˜50 bp repeat sequence length versus ˜500 bp repeat sequence length in previous reports). This difference in repeat sequence length in the concatemers of the library allows for the generation of highly complex libraries of candidate nuclease target sites, e.g., of libraries comprising 10¹² different candidate nuclease target sequences. As described herein, an exemplary library of such complexity has been generated, templated on a known Cas9 nuclease target site by varying the sequence of the known target site. The exemplary library demonstrated that a greater than 10-fold coverage of all sequences with eight or fewer mutations of the known target site can be achieved using the strategies provided herein. The use of a shorter repeat sequence also allows the use of single-end sequencing, since both a cut half-site and an adjacent uncut site of the same library member are contained within a 100 nucleotide sequencing read.

The strategies, methods, libraries, and reagents provided herein can be utilized to analyze the sequence preferences and specificity of any site-specific nuclease, for example, to Zinc Finger Nucleases (ZFNs), Transcription Activator-Like Effector Nucleases (TALENs), homing endonucleases, organic compound nucleases, and enediyne antibiotics (e.g., dynemicin, neocarzinostatin, calicheamicin, esperamicin, bleomycin). Suitable nucleases in addition to the ones described herein will be apparent to those of skill in the art based on this disclosure.

Further, the methods, reagents, and strategies provided herein allow those of skill in the art to identify, design, and/or select nucleases with enhanced specificity and minimize the off-target effects of any given nuclease (e.g., site-specific nucleases such as ZFNs, and TALENS which produce cleavage products with sticky ends, as well as RNA-programmable nucleases, for example Cas9, which produce cleavage products having blunt ends). While of particular relevance to DNA and DNA-cleaving nucleases, the inventive concepts, methods, strategies, and reagents provided herein are not limited in this respect, but can be applied to any nucleic acid:nuclease pair.

Identifying Nuclease Target Sites Cleaved by a Site-Specific Nuclease

Some aspects of this disclosure provide improved methods and reagents to determine the nucleic acid target sites cleaved by any site-specific nuclease. The methods provided herein can be used for the evaluation of target site preferences and specificity of both nucleases that create blunt ends and nucleases that create sticky ends. In general, such methods comprise contacting a given nuclease with a library of target sites under conditions suitable for the nuclease to bind and cut a target site, and determining which target sites the nuclease actually cuts. A determination of a nuclease's target site profile based on actual cutting has the advantage over methods that rely on binding in that it measures a parameter more relevant for mediating undesired off-target effects of site-specific nucleases. In general, the methods provided herein comprise ligating an adapter of a known sequence to nucleic acid molecules that have been cut by a nuclease of interest via 5′-phosphate-dependent ligation. Accordingly, the methods provided herein are particularly useful for identifying target sites cut by nucleases that leave a phosphate moiety at the 5′-end of the cut nucleic acid strand when cleaving their target site. After ligating an adapter to the 5′-end of a cut nucleic acid strand, the cut strand can directly be sequenced using the adapter as a sequencing linker, or a part of the cut library member concatemer comprising an intact target site identical to the cut target site can be amplified via PCR and the amplification product can then be sequenced.

In some embodiments, the method comprises (a) providing a nuclease that cuts a double-stranded nucleic acid target site, wherein cutting of the target site results in cut nucleic acid strands comprising a 5′-phosphate moiety; (b) contacting the nuclease of (a) with a library of candidate nucleic acid molecules, wherein each nucleic acid molecule comprises a concatemer of a sequence comprising a candidate nuclease target site and a constant insert sequence, under conditions suitable for the nuclease to cut a candidate nucleic acid molecule comprising a target site of the nuclease; and (c) identifying nuclease target sites cut by the nuclease in (b) by determining the sequence of an uncut nuclease target site on the nucleic acid strand that was cut by the nuclease in step (b).

In some embodiments, the method comprises providing a nuclease and contacting the nuclease with a library of candidate nucleic acid molecules comprising candidate target sites. In some embodiments, the candidate nucleic acid molecules are double-stranded nucleic acid molecules. In some embodiments, the candidate nucleic acid molecules are DNA molecules. In some embodiments, each nucleic acid molecule in the library comprises a concatemer of a sequence comprising a candidate nuclease target site and a constant insert sequence. For example, in some embodiments, the library comprises nucleic acid molecules that comprise the structure R₁-[(candidate nuclease target site)-(constant insert sequence)]_(n)-R₂, wherein R₁ and R₂ are, independently, nucleic acid sequences that may comprise a fragment of the [(candidate nuclease target site)-(constant insert sequence)] structure, and n is an integer between 2 and y. In some embodiments, y is at least 10¹, at least 10², at least 10³, at least 10⁴, at least 10⁵, at least 10⁶, at least 10⁷, at least 10⁸, at least 10⁹, at least 10¹⁰, at least 10¹¹, at least 10¹², at least 10¹³, at least 10¹⁴, or at least 10¹⁵. In some embodiments, y is less than 10², less than 10³, less than 10⁴, less than 10⁵, less than 10⁶, less than 10⁷, less than 10⁸, less than 10⁹, less than 10¹⁰, less than 10¹¹, less than 10¹², less than 10¹³, less than 10¹⁴, or less than 10¹⁵

For example, in some embodiments, the candidate nucleic acid molecules of the library comprise a candidate nuclease target site of the structure [(N_(Z))-(PAM)], and, thus, the nucleic acid molecules of the library comprise the structure R₁-[(N_(Z))-(PAM)-(constant region)]_(X)-R₂, wherein R₁ and R₂ are, independently, nucleic acid sequences that may comprise a fragment of the [(N_(Z))-(PAM)-(constant region)] repeat unit; each N represents, independently, any nucleotide; Z is an integer between 1 and 50; and X is an integer between 2 and y. In some embodiments, y is at least 10¹, at least 10², at least 10³, at least 10⁴, at least 10⁵, at least 10⁶, at least 10⁷, at least 10⁸, at least 10⁹, at least 10¹⁰, at least 10¹¹, at least 10¹², at least 10¹³, at least 10¹⁴, or at least 10¹⁵. In some embodiments, y is less than 10², less than 10³, less than 10⁴, less than 10⁵, less than 10⁶, less than 10⁷, less than 10⁸, less than 10⁹, less than 10¹⁰, less than 10¹¹, less than 10¹², less than 10¹³, less than 10¹⁴, or less than 10¹⁵. In some embodiments, Z is at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50. In some embodiments, Z is 20. Each N represents, independently, any nucleotide. Accordingly, a sequence provided as N_(Z) with _(Z)=2 would be NN, with each N, independently, representing A, T, G, or C. Accordingly, N_(Z) with _(Z)=2 can represent AA, AT, AG, AC, TA, TT, TG, TC, GA, GT, GG, GC, CA, CT, CG, and CC.

In other embodiments, the candidate nucleic acid molecules of the library comprise a candidate nuclease target site of the structure [left-half site]-[spacer sequence]-[right-half site] (“LSR”), and, thus, the nucleic acid molecules of the library comprise the structure R₁-[(LSR)-(constant region)]_(X)-R₂, wherein R₁ and R₂ are, independently, nucleic acid sequences that may comprise a fragment of the [(LSR)-(constant region)] repeat unit, and X is an integer between 2 and y. In some embodiments, y is at least 10¹, at least 10², at least 10³, at least 10⁴, at least 10⁵, at least 10⁶, at least 10⁷, at least 10⁸, at least 10⁹, at least 10¹⁰, at least 10¹¹, at least 10¹², at least 10¹³, at least 10¹⁴, or at least 10¹⁵. In some embodiments, y is less than 10², less than 10³, less than 10⁴, less than 10⁵, less than 10⁶, less than 10⁷, less than 10⁸, less than 10⁹, less than 10¹⁰, less than 10¹¹, less than 10¹², less than 10¹³, less than 10¹⁴, or less than 10¹⁵. The constant region, in some embodiments, is of a length that allows for efficient self-ligation of a single repeat unit. Suitable lengths will be apparent to those of skill in the art. For example, in some embodiments, the constant region is between 5 and 100 base pairs long, for example, about 5 base pairs, about 10 base pairs, about 15 base pairs, about 20 base pairs, about 25 base pairs, about 30 base pairs, about 35 base pairs, about 40 base pairs, about 50 base pairs, about 60 base pairs, about 70 base pairs, about 80 base pairs, about 90 base pairs, or about 100 base pairs long. In some embodiments, the constant region is 16 base pairs long. In some embodiments, the nuclease cuts a double-stranded nucleic acid target site and creates blunt ends. In other embodiments, the nuclease creates a 5′-overhang. In some such embodiments, the target site comprises a [left-half site]-[spacer sequence]-[right-half site] (LSR) structure, and the nuclease cuts the target site within the spacer sequence.

In some embodiments, a nuclease cuts a double-stranded target site and creates blunt ends. In some embodiments, a nuclease cuts a double-stranded target site and creates an overhang, or sticky end, for example, a 5′-overhang. In some such embodiments, the method comprises filling in the 5′-overhangs of nucleic acid molecules produced from a nucleic acid molecule that has been cut once by the nuclease, wherein the nucleic acid molecules comprise a constant insert sequence flanked by a left or right half-site and cut spacer sequence on one side, and an uncut target site sequence on the other side, thereby creating blunt ends.

In some embodiments, the determining of step (c) comprises ligating a first nucleic acid adapter to the 5′ end of a nucleic acid strand that was cut by the nuclease in step (b) via 5′-phosphate-dependent ligation. In some embodiments, the nuclease creates blunt ends. In such embodiments, an adapter can directly be ligated to the blunt ends resulting from the nuclease cut of the target site by contacting the cut library members with a double-stranded, blunt-ended adapter lacking 5′ phosphorylation. In some embodiments, the nuclease creates an overhang (sticky end). In some such embodiments, an adapter may be ligated to the cut site by contacting the cut library member with an excess of adapter having a compatible sticky end. If a nuclease is used that cuts within a constant spacer sequence between variable half-sites, the sticky end can be designed to match the 5′ overhang created from the spacer sequence. In embodiments, where the nuclease cuts within a variable sequence, a population of adapters having a variable overhang sequence and a constant annealed sequence (for use as a sequencing linker or PCR primer) may be used, or the 5′ overhangs may be filled in to form blunt ends before adapter ligation.

In some embodiments, the determining of step (c) further comprises amplifying a fragment of the concatemer cut by the nuclease that comprises an uncut target site via PCR using a PCR primer that hybridizes with the adapter and a PCR primer that hybridizes with the constant insert sequence. Typically, the amplification of concatemers via PCR will yield amplicons comprising at least one intact candidate target site identical to the cut target sites because the target sites in each concatemer are identical. For single-direction sequencing, an enrichment of amplicons that comprise one intact target site, no more than two intact target sites, no more than three intact target sites, no more than four intact target sites, or no more than five intact target sites may be desirable. In embodiments where PCR is used for amplification of cut nucleic acid molecules, the PCR parameters can be optimized to favor the amplification of short sequences and disfavor the amplification of longer sequences, e.g., by using a short elongation time in the PCR cycle. Another possibility for enrichment of short amplicons is size fractionation, e.g., via gel electrophoresis or size exclusion chromatography. Size fractionation can be performed before and/or after amplification. Other suitable methods for enrichment of short amplicons will be apparent to those of skill in the art and the disclosure is not limited in this respect.

In some embodiments, the determining of step (c) comprises sequencing the nucleic acid strand that was cut by the nuclease in step (b), or a copy thereof obtained via amplification, e.g., by PCR. Sequencing methods are well known to those of skill in the art. The disclosure is not limited in this respect.

In some embodiments, the nuclease being profiled using the inventive system is an RNA-programmable nuclease that forms a complex with an RNA molecule, and wherein the nuclease:RNA complex specifically binds a nucleic acid sequence complementary to the sequence of the RNA molecule. In some embodiments, the RNA molecule is a single-guide RNA (sgRNA). In some embodiments, the sgRNA comprises 5-50 nucleotides, 10-30 nucleotides, 15-25 nucleotides, 18-22 nucleotides, 19-21 nucleotides, e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, the sgRNA comprises 5-50 nucleotides, 10-30 nucleotides, 15-25 nucleotides, 18-22 nucleotides, 19-21 nucleotides, e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides that are complementary to a sequence of the nuclease target site. In some embodiments, the sgRNA comprises 20 nucleotides that are complementary to the nuclease target site. In some embodiments, the nuclease is a Cas9 nuclease. In some embodiments, the nuclease target site comprises a [sgRNA-complementary sequence]-[protospacer adjacent motif (PAM)] structure, and the nuclease cuts the target site within the sgRNA-complementary sequence. In some embodiments, the sgRNA-complementary sequence comprises 5-50 nucleotides, 10-30 nucleotides, 15-25 nucleotides, 18-22 nucleotides, 19-21 nucleotides, e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.

In some embodiments, the RNA-programmable nuclease is a Cas9 nuclease. The RNA-programmable Cas9 endonuclease cleaves double-stranded DNA (dsDNA) at sites adjacent to a two-base-pair PAM motif and complementary to a guide RNA sequence (sgRNA). Typically, the sgRNA sequence that is complementary to the target site sequence is about 20 nucleotides long, but shorter and longer complementary sgRNA sequences can be used as well. For example, in some embodiments, the sgRNA comprises 5-50 nucleotides, 10-30 nucleotides, 15-25 nucleotides, 18-22 nucleotides, 19-21 nucleotides, e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. The Cas9 system has been used to modify genomes in multiple cell types, demonstrating its potential as a facile genome-engineering tool.

In some embodiments, the nuclease comprises an unspecific nucleic acid cleavage domain. In some embodiments, the nuclease comprises a FokI cleavage domain. In some embodiments, the nuclease comprises a nucleic acid cleavage domain that cleaves a target sequence upon cleavage domain dimerization. In some embodiments, the nuclease comprises a binding domain that specifically binds a nucleic acid sequence. In some embodiments, the binding domain comprises a zinc finger. In some embodiments, the binding domain comprises at least 2, at least 3, at least 4, or at least 5 zinc fingers. In some embodiments, the nuclease is a Zinc Finger Nuclease. In some embodiments, the binding domain comprises a Transcriptional Activator-Like Element. In some embodiments, the nuclease is a Transcriptional Activator-Like Element Nuclease (TALEN). In some embodiments, the nuclease is a homing endonuclease. In some embodiments, the nuclease is an organic compound. In some embodiments, the nuclease comprises an enediyne functional group. In some embodiments, the nuclease is an antibiotic. In some embodiments, the compound is dynemicin, neocarzinostatin, calicheamicin, esperamicin, bleomycin, or a derivative thereof.

Incubation of the nuclease with the library nucleic acids will result in cleavage of those concatemers in the library that comprise target sites that can be bound and cleaved by the nuclease. If a given nuclease cleaves a specific target site with high efficiency, a concatemer comprising target sites will be cut, e.g., once or multiple times, resulting in the generation of fragments comprising a cut target site adjacent to one or more repeat units. Depending on the structure of the library members, an exemplary cut nucleic acid molecule released from a library member concatemer by a single nuclease cleavage may, for example, be of the structure (cut target site)-(constant region)-[(target site)-(constant region)]_(X)-R₂. For example, in the context of an RNA-guided nuclease, an exemplary cut nucleic acid molecule released from a library member concatemer by a single nuclease cleavage may, for example, be of the structure (PAM)-(constant region)-[(N_(Z))-(PAM)-(constant region)]_(X)-R₂. And in the context of a nuclease cutting an LSR structure within the spacer region, an exemplary cut nucleic acid molecule released from a library member concatemer by a single nuclease cleavage may, for example, be of the structure (cut spacer region)-(right half site)-(constant region)-[(LSR)-(constant region)]_(X)-R₂. Such cut fragments released from library candidate molecules can then be isolated and/or the sequence of the target site cleaved by the nuclease identified by sequencing an intact target site (e.g., an intact (N_(Z))-(PAM) site of released repeat units. See, e.g., FIG. 1B for an illustration.

Suitable conditions for exposure of the library of nucleic acid molecules will be apparent to those of skill in the art. In some embodiments, suitable conditions do not result in denaturation of the library nucleic acids or the nuclease and allow for the nuclease to exhibit at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or at least 98% of its nuclease activity.

Additionally, if a given nuclease cleaves a specific target site, some cleavage products will comprise a cut half site and an intact, or uncut target site. As described herein, such products can be isolated by routine methods, and because the insert sequence, in some aspects, is less than 100 base pairs, such isolated cleavage products may be sequenced in a single read-through, allowing identification of the target site sequence without reconstructing the sequence, e.g., from cut half sites.

Any method suitable for isolation and sequencing of the repeat units can be employed to elucidate the LSR sequence cleaved by the nuclease. For example, since the length of the constant region is known, individual released repeat units can be separated based on their size from the larger uncut library nucleic acid molecules as well as from fragments of library nucleic acid molecules that comprise multiple repeat units (indicating non-efficient targeted cleavage by the nuclease). Suitable methods for separating and/or isolating nucleic acid molecules based on their size are well-known to those of skill in the art and include, for example, size fractionation methods, such as gel electrophoresis, density gradient centrifugation, and dialysis over a semi-permeable membrane with a suitable molecular cutoff value. The separated/isolated nucleic acid molecules can then be further characterized, for example, by ligating PCR and/or sequencing adapters to the cut ends and amplifying and/or sequencing the respective nucleic acids. Further, if the length of the constant region is selected to favor self-ligation of individual released repeat units, such individual released repeat units may be enriched by contacting the nuclease treated library molecules with a ligase and subsequent amplification and/or sequencing based on the circularized nature of the self-ligated individual repeat units.

In some embodiments, where a nuclease is used that generates 5′-overhangs as a result of cutting a target nucleic acid, the 5′-overhangs of the cut nucleic acid molecules are filled in. Methods for filling in 5′-overhangs are well known to those of skill in the art and include, for example, methods using DNA polymerase I Klenow fragment lacking exonuclease activity (Klenow (3′→5′ exo-)). Filling in 5′-overhangs results in the overhang-templated extension of the recessed strand, which, in turn, results in blunt ends. In the case of single repeat units released from library concatemers, the resulting structure is a blunt-ended S₂′R-(constant region)-LS₁′, with S₁′ and S₂′ comprising blunt ends. PCR and/or sequencing adapters can then be added to the ends by blunt end ligation and the respective repeat units (including S₂′R and LS₁′ regions) can be sequenced. From the sequence data, the original LSR region can be deduced. Blunting of the overhangs created during the nuclease cleavage process also allows for distinguishing between target sites that were properly cut by the respective nuclease and target sites that were non-specifically cut, e.g., based on non-nuclease effects such as physical shearing. Correctly cleaved nuclease target sites can be recognized by the existence of complementary S₂′R and LS₁′ regions, which comprise a duplication of the overhang nucleotides as a result of the overhang fill in while target sites that were not cleaved by the respective nuclease are unlikely to comprise overhang nucleotide duplications. In some embodiments, the method comprises identifying the nuclease target site cut by the nuclease by determining the sequence of the left-half site, the right-half-site, and/or the spacer sequence of a released individual repeat unit. Any suitable method for amplifying and/or sequencing can be used to identify the LSR sequence of the target site cleaved by the respective nuclease. Methods for amplifying and/or sequencing nucleic acids are well known to those of skill in the art and the disclosure is not limited in this respect. In the case of nucleic acids released from library concatemers that comprise a cut half site and an uncut target site (e.g., comprises at least about 1.5 repeat sequences), filling in the 5′-overhangs also provides for assurance that the nucleic acid was cleaved by the nuclease. Because the nucleic acid also comprises an intact, or uncut target site, the sequence of said site can be determined without having to reconstruct the sequence from a left-half site, right-half site, and/or spacer sequence.

Some of the methods and strategies provided herein allow for the simultaneous assessment of a plurality of candidate target sites as possible cleavage targets for any given nuclease. Accordingly, the data obtained from such methods can be used to compile a list of target sites cleaved by a given nuclease, which is also referred to herein as a target site profile. If a sequencing method is used that allows for the generation of quantitative sequencing data, it is also possible to record the relative abundance of any nuclease target site detected to be cleaved by the respective nuclease. Target sites that are cleaved more efficiently by the nuclease will be detected more frequently in the sequencing step, while target sites that are not cleaved efficiently will only rarely release an individual repeat unit from a candidate concatemer, and thus, will only generate few, if any, sequencing reads. Such quantitative sequencing data can be integrated into a target site profile to generate a ranked list of highly preferred and less preferred nuclease target sites.

The methods and strategies of nuclease target site profiling provided herein can be applied to any site-specific nuclease, including, for example, ZFNs, TALENs, homing endonucleases, and RNA-programmable nucleases, such as Cas9 nucleases. As described in more detail herein, nuclease specificity typically decreases with increasing nuclease concentration, and the methods described herein can be used to determine a concentration at which a given nuclease efficiently cuts its intended target site, but does not efficiently cut any off-target sequences. In some embodiments, a maximum concentration of a therapeutic nuclease is determined at which the therapeutic nuclease cuts its intended nuclease target site but does not cut more than 10, more than 5, more than 4, more than 3, more than 2, more than 1, or any additional sites. In some embodiments, a therapeutic nuclease is administered to a subject in an amount effective to generate a final concentration equal or lower than the maximum concentration determined as described above.

In some embodiments, the library of candidate nucleic acid molecules used in the methods provided herein comprises at least 10⁸, at least 10⁹, at least 10¹⁰, at least 10¹¹, or at least 10¹² different candidate nuclease target sites.

In some embodiments, the nuclease is a therapeutic nuclease which cuts a specific nuclease target site in a gene associated with a disease. In some embodiments, the method further comprises determining a maximum concentration of the therapeutic nuclease at which the therapeutic nuclease cuts the specific nuclease target site and does not cut more than 10, more than 5, more than 4, more than 3, more than 2, more than 1, or no additional sites. In some embodiments, the method further comprises administering the therapeutic nuclease to a subject in an amount effective to generate a final concentration equal or lower than the maximum concentration.

Nuclease Target Site Libraries

Some embodiments of this disclosure provide libraries of nucleic acid molecules for nuclease target site profiling. In some embodiments, the candidate nucleic acid molecules of the library comprise the structure R₁-[(N_(Z))-(PAM)-(constant region)]_(X)-R₂, wherein R₁ and R₂ are, independently, nucleic acid sequences that may comprise a fragment of the [(N_(Z))-(PAM)-(constant region)] repeat unit; each N represents, independently, any nucleotide; Z is an integer between 1 and 50; and X is an integer between 2 and y. In some embodiments, y is at least 10¹, at least 10², at least 10³, at least 10⁴, at least 10⁵, at least 10⁶, at least 10⁷, at least 10⁸, at least 10⁹, at least 10¹⁰, at least 10¹¹, at least 10¹², at least 10¹³, at least 10¹⁴, or at least 10¹⁵. In some embodiments, y is less than 10², less than 10³, less than 10⁴, less than 10⁵, less than 10⁶, less than 10⁷, less than 10⁸, less than 10⁹, less than 10¹⁰, less than 10¹¹, less than 10¹², less than 10¹³, less than 10¹⁴, or less than 10¹⁵. In some embodiments, Z is at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50. In some embodiments, Z is 20. Each N represents, independently, any nucleotide. Accordingly, a sequence provided as N_(Z) with _(Z)=2 would be NN, with each N, independently, representing A, T, G, or C. Accordingly, N_(Z) with _(Z)=2 can represent AA, AT, AG, AC, TA, TT, TG, TC, GA, GT, GG, GC, CA, CT, CG, and CC.

In some embodiments, a library is provided comprising candidate nucleic acid molecules that comprise target sites with a partially randomized left-half site, a partially randomized right-half site, and/or a partially randomized spacer sequence. In some embodiments, the library is provided comprising candidate nucleic acid molecules that comprise target sites with a partially randomized left half site, a fully randomized spacer sequence, and a partially randomized right half site. In some embodiments, a library is provided comprising candidate nucleic acid molecules that comprise target sites with a partially or fully randomized sequence, wherein the target sites comprise the structure [N_(Z)-(PAM)], for example as described herein. In some embodiments, partially randomized sites differ from the consensus site by more than 5%, more than 10%, more than 15%, more than 20%, more than 25%, or more than 30% on average, distributed binomially.

In some embodiments such a library comprises a plurality of nucleic acid molecules, each comprising a concatemer of a candidate nuclease target site and a constant insert sequence, also referred to herein as a constant region. For example, in some embodiments, the candidate nucleic acid molecules of the library comprise the structure R₁-[(sgRNA-complementary sequence)-(PAM)-(constant region)]_(X)-R₂, or the structure R₁-[(LSR)-(constant region)]_(X)-R₂, wherein the structure in square brackets (“[ . . . ]”) is referred to as a repeat unit or repeat sequence; R₁ and R₂ are, independently, nucleic acid sequences that may comprise a fragment of the repeat unit, and X is an integer between 2 and y. In some embodiments, y is at least 10¹, at least 10², at least 10³, at least 10⁴, at least 10⁵, at least 10⁶, at least 10⁷, at least 10⁸, at least 10⁹, at least 10¹⁰, at least 10¹¹, at least 10¹², at least 10¹³, at least 10¹⁴, or at least 10¹⁵. In some embodiments, y is less than 10², less than 10³, less than 10⁴, less than 10⁵, less than 10⁶, less than 10⁷, less than 10⁸, less than 10⁹, less than 10¹⁰, less than 10¹¹, less than 10¹², less than 10¹³, less than 10¹⁴, or less than 10¹⁵. The constant region, in some embodiments, is of a length that allows for efficient self-ligation of a single repeat unit. In some embodiments, the constant region is of a length that allows for efficient separation of single repeat units from fragments comprising two or more repeat units. In some embodiments, the constant region is of a length allows for efficient sequencing of a complete repeat unit in one sequencing read. Suitable lengths will be apparent to those of skill in the art. For example, in some embodiments, the constant region is between 5 and 100 base pairs long, for example, about 5 base pairs, about 10 base pairs, about 15 base pairs, about 20 base pairs, about 25 base pairs, about 30 base pairs, about 35 base pairs, about 40 base pairs, about 50 base pairs, about 60 base pairs, about 70 base pairs, about 80 base pairs, about 90 base pairs, or about 100 base pairs long. In some embodiments, the constant region is 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, or 80 base pairs long.

An LSR site typically comprises a [left-half site]-[spacer sequence]-[right-half site] structure. The lengths of the half-size and the spacer sequence will depend on the specific nuclease to be evaluated. In general, the half-sites will be 6-30 nucleotides long, and preferably 10-18 nucleotides long. For example, each half site individually may be 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides long. In some embodiments, an LSR site may be longer than 30 nucleotides. In some embodiments, the left half site and the right half site of an LSR are of the same length. In some embodiments, the left half site and the right half site of an LSR are of different lengths. In some embodiments, the left half site and the right half site of an LSR are of different sequences. In some embodiments, a library is provided that comprises candidate nucleic acids which comprise LSRs that can be cleaved by a FokI cleavage domain, a Zinc Finger Nuclease (ZFN), a Transcription Activator-Like Effector Nuclease (TALEN), a homing endonuclease, or an organic compound (e.g., an enediyne antibiotic such as dynemicin, neocarzinostatin, calicheamicin, and esperamicinl; and bleomycin).

In some embodiments, a library of candidate nucleic acid molecules is provided that comprises at least 10⁵, at least 10⁶, at least 10⁷, at least 10⁸, at least 10⁹, at least 10¹⁰, at least 10¹¹, at least 10¹², at least 10¹³, at least 10¹⁴, or at least 10¹⁵ different candidate nuclease target sites. In some embodiments, the candidate nucleic acid molecules of the library are concatemers produced from a secularized templates by rolling cycle amplification. In some embodiments, the library comprises nucleic acid molecules, e.g., concatemers, of a molecular weight of at least 5 kDa, at least 6 kDa, at least 7 kDa, at least 8 kDa, at least 9 kDa, at least 10 kDa, at least 12 kDa, or at least 15 kDa. In some embodiments, the molecular weight of the nucleic acid molecules within the library may be larger than 15 kDa. In some embodiments, the library comprises nucleic acid molecules within a specific size range, for example, within a range of 5-7 kDa, 5-10 kDa, 8-12 kDa, 10-15 kDa, or 12-15 kDa, or 5-10 kDa or any possible subrange. While some methods suitable for generating nucleic acid concatemers according to some aspects of this disclosure result in the generation of nucleic acid molecules of greatly different molecular weights, such mixtures of nucleic acid molecules may be size fractionated to obtain a desired size distribution. Suitable methods for enriching nucleic acid molecules of a desired size or excluding nucleic acid molecules of a desired size are well known to those of skill in the art and the disclosure is not limited in this respect.

In some embodiments, partially randomized sites differ from the consensus site by no more than 10%, no more than 15%, no more than 20%, no more than 25%, nor more than 30%, no more than 40%, or no more than 50% on average, distributed binomially. For example, in some embodiments partially randomized sites differ from the consensus site by more than 5%, but by no more than 10%; by more than 10%, but by no more than 20%; by more than 20%, but by no more than 25%; by more than 5%, but by no more than 20%, and so on. Using partially randomized nuclease target sites in the library is useful to increase the concentration of library members comprising target sites that are closely related to the consensus site, for example, that differ from the consensus sites in only one, only two, only three, only four, or only five residues. The rationale behind this is that a given nuclease, for example a given ZFN or RNA-programmable nuclease, is likely to cut its intended target site and any closely related target sites, but unlikely to cut a target sites that is vastly different from or completely unrelated to the intended target site. Accordingly, using a library comprising partially randomized target sites can be more efficient than using libraries comprising fully randomized target sites without compromising the sensitivity in detecting any off-target cleavage events for any given nuclease. Thus, the use of partially randomized libraries significantly reduces the cost and effort required to produce a library having a high likelihood of covering virtually all off-target sites of a given nuclease. In some embodiments however it may be desirable to use a fully randomized library of target sites, for example, in embodiments, where the specificity of a given nuclease is to be evaluated in the context of any possible site in a given genome.

Selection and Design of Site-Specific Nucleases

Some aspects of this disclosure provide methods and strategies for selecting and designing site-specific nucleases that allow the targeted cleavage of a single, unique sites in the context of a complex genome. In some embodiments, a method is provided that comprises providing a plurality of candidate nucleases that are designed or known to cut the same consensus sequence; profiling the target sites actually cleaved by each candidate nuclease, thus detecting any cleaved off-target sites (target sites that differ from the consensus target site); and selecting a candidate nuclease based on the off-target site(s) so identified. In some embodiments, this method is used to select the most specific nuclease from a group of candidate nucleases, for example, the nuclease that cleaves the consensus target site with the highest specificity, the nuclease that cleaves the lowest number of off-target sites, the nuclease that cleaves the lowest number of off-target sites in the context of a target genome, or a nuclease that does not cleave any target site other than the consensus target site. In some embodiments, this method is used to select a nuclease that does not cleave any off-target site in the context of the genome of a subject at concentration that is equal to or higher than a therapeutically effective concentration of the nuclease.

The methods and reagents provided herein can be used, for example, to evaluate a plurality of different nucleases targeting the same intended targets site, for example, a plurality of variations of a given site-specific nuclease, for example a given zinc finger nuclease. Accordingly, such methods may be used as the selection step in evolving or designing a novel site-specific nucleases with improved specificity.

Identifying Unique Nuclease Target Sites within a Genome

Some embodiments of this disclosure provide a method for selecting a nuclease target site within a genome. As described in more detail elsewhere herein, it was surprisingly discovered that off target sites cleaved by a given nuclease are typically highly similar to the consensus target site, e.g., differing from the consensus target site in only one, only two, only three, only four, or only five nucleotide residues. Based on this discovery, a nuclease target sites within the genome can be selected to increase the likelihood of a nuclease targeting this site not cleaving any off target sites within the genome. For example, in some embodiments, a method is provided that comprises identifying a candidate nuclease target site; and comparing the candidate nuclease target site to other sequences within the genome. Methods for comparing candidate nuclease target sites to other sequences within the genome are well known to those of skill in the art and include for example sequence alignment methods, for example, using a sequence alignment software or algorithm such as BLAST on a general purpose computer. A suitable unique nuclease target site can then be selected based on the results of the sequence comparison. In some embodiments, if the candidate nuclease target site differs from any other sequence within the genome by at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10 nucleotides, the nuclease target site is selected as a unique site within the genome, whereas if the site does not fulfill this criteria, the site may be discarded. In some embodiments, once a site is selected based on the sequence comparison, as outlined above, a site-specific nuclease targeting the selected site is designed. For example, a zinc finger nuclease may be designed to target any selected nuclease target site by constructing a zinc finger array binding the target site, and conjugating the zinc finger array to a DNA cleavage domain. In embodiments where the DNA cleavage domain needs to dimerize in order to cleave DNA, to zinc finger arrays will be designed, each binding a half site of the nuclease target site, and each conjugated to a cleavage domain. In some embodiments, nuclease designing and/or generating is done by recombinant technology. Suitable recombinant technologies are well known to those of skill in the art, and the disclosure is not limited in this respect.

In some embodiments, a site-specific nuclease designed or generated according to aspects of this disclosure is isolated and/or purified. The methods and strategies for designing site-specific nucleases according to aspects of this disclosure can be applied to design or generate any site-specific nuclease, including, but not limited to Zinc Finger Nucleases, Transcription Activator-Like Effector Nucleases (TALENs), a homing endonuclease, an organic compound nuclease, or an enediyne antibiotic (e.g., dynemicin, neocarzinostatin, calicheamicin, esperamicin, bleomycin).

Isolated Nucleases

Some aspects of this disclosure provide isolated site-specific nucleases with enhanced specificity that are designed using the methods and strategies described herein. Some embodiments, of this disclosure provide nucleic acids encoding such nucleases. Some embodiments of this disclosure provide expression constructs comprising such encoding nucleic acids. For example, in some embodiments an isolated nuclease is provided that has been engineered to cleave a desired target site within a genome, and has been evaluated according to a method provided herein to cut less than 1, less than 2, less than 3, less than 4, less than 5, less than 6, less than 7, less than 8, less than 9 or less than 10 off-target sites at a concentration effective for the nuclease to cut its intended target site. In some embodiments an isolated nuclease is provided that has been engineered to cleave a desired unique target site that has been selected to differ from any other site within a genome by at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10 nucleotide residues. In some embodiments, the isolated nuclease is an RNA-programmable nuclease, such as a Cas9 nuclease; a Zinc Finger Nuclease (ZFN); or a Transcription Activator-Like Effector Nuclease (TALEN), a homing endonuclease, an organic compound nuclease, or an enediyne antibiotic (e.g., dynemicin, neocarzinostatin, calicheamicin, esperamicin, bleomycin). In some embodiments, the isolated nuclease cleaves a target site within an allele that is associated with a disease or disorder. In some embodiments, the isolated nuclease cleaves a target site the cleavage of which results in treatment or prevention of a disease or disorder. In some embodiments, the disease is HIV/AIDS, or a proliferative disease. In some embodiments, the allele is a CCR5 (for treating HIV/AIDS) or a VEGFA allele (for treating a proliferative disease).

In some embodiments, the isolated nuclease is provided as part of a pharmaceutical composition. For example, some embodiments provide pharmaceutical compositions comprising a nuclease as provided herein, or a nucleic acid encoding such a nuclease, and a pharmaceutically acceptable excipient. Pharmaceutical compositions may optionally comprise one or more additional therapeutically active substances.

In some embodiments, compositions provided herein are administered to a subject, for example, to a human subject, in order to effect a targeted genomic modification within the subject. In some embodiments, cells are obtained from the subject and contacted with a nuclease or a nuclease-encoding nucleic acid ex vivo, and re-administered to the subject after the desired genomic modification has been effected or detected in the cells. Although the descriptions of pharmaceutical compositions provided herein are principally directed to pharmaceutical compositions which are suitable for administration to humans, it will be understood by the skilled artisan that such compositions are generally suitable for administration to animals of all sorts. Modification of pharmaceutical compositions suitable for administration to humans in order to render the compositions suitable for administration to various animals is well understood, and the ordinarily skilled veterinary pharmacologist can design and/or perform such modification with merely ordinary, if any, experimentation. Subjects to which administration of the pharmaceutical compositions is contemplated include, but are not limited to, humans and/or other primates; mammals, including commercially relevant mammals such as cattle, pigs, horses, sheep, cats, dogs, mice, and/or rats; and/or birds, including commercially relevant birds such as chickens, ducks, geese, and/or turkeys.

Formulations of the pharmaceutical compositions described herein may be prepared by any method known or hereafter developed in the art of pharmacology. In general, such preparatory methods include the step of bringing the active ingredient into association with an excipient and/or one or more other accessory ingredients, and then, if necessary and/or desirable, shaping and/or packaging the product into a desired single- or multi-dose unit.

Pharmaceutical formulations may additionally comprise a pharmaceutically acceptable excipient, which, as used herein, includes any and all solvents, dispersion media, diluents, or other liquid vehicles, dispersion or suspension aids, surface active agents, isotonic agents, thickening or emulsifying agents, preservatives, solid binders, lubricants and the like, as suited to the particular dosage form desired. Remington's The Science and Practice of Pharmacy, 21^(st) Edition, A. R. Gennaro (Lippincott, Williams & Wilkins, Baltimore, Md., 2006; incorporated in its entirety herein by reference) discloses various excipients used in formulating pharmaceutical compositions and known techniques for the preparation thereof. See also PCT application PCT/US2010/055131, incorporated in its entirety herein by reference, for additional suitable methods, reagents, excipients and solvents for producing pharmaceutical compositions comprising a nuclease. Except insofar as any conventional excipient medium is incompatible with a substance or its derivatives, such as by producing any undesirable biological effect or otherwise interacting in a deleterious manner with any other component(s) of the pharmaceutical composition, its use is contemplated to be within the scope of this disclosure.

The function and advantage of these and other embodiments of the present invention will be more fully understood from the Examples below. The following Examples are intended to illustrate the benefits of the present invention and to describe particular embodiments, but are not intended to exemplify the full scope of the invention. Accordingly, it will be understood that the Examples are not meant to limit the scope of the invention.

EXAMPLES Materials and Methods

Oligonucleotides. All oligonucleotides used in this study were purchased from Integrated DNA Technologies. Oligonucleotide sequences are listed in Table 9.

Expression and Purification of S. pyogenes Cas9. E. coli Rosetta (DE3) cells were transformed with plasmid pMJ806¹¹, encoding the S. pyogenes cas9 gene fused to an N-terminal 6×His-tag/maltose binding protein. The resulting expression strain was inoculated in Luria-Bertani (LB) broth containing 100 μg/mL of ampicillin and 30 μg/mL of chloramphenicol at 37° C. overnight. The cells were diluted 1:100 into the same growth medium and grown at 37° C. to OD₆₀₀˜0.6. The culture was incubated at 18° C. for 30 min, and isopropyl β-D-1-thiogalactopyranoside (IPTG) was added at 0.2 mM to induce Cas9 expression. After ˜17 h, the cells were collected by centrifugation at 8,000 g and resuspended in lysis buffer (20 mM tris(hydroxymethyl)-aminomethane (Tris)-HCl, pH 8.0, 1 M KCl, 20% glycerol, 1 mM tris (2-carboxyethyl)phosphine (TCEP)). The cells were lysed by sonication (10 sec pulse-on and 30 sec pulse-off for 10 min total at 6 W output) and the soluble lysate was obtained by centrifugation at 20,000 g for 30 min. The cell lysate was incubated with nickel-nitriloacetic acid (nickel-NTA) resin (Qiagen) at 4° C. for 20 min to capture His-tagged Cas9. The resin was transferred to a 20-mL column and washed with 20 column volumes of lysis buffer. Cas9 was eluted in 20 mM Tris-HCl (pH 8), 0.1 M KCl, 20% glycerol, 1 mM TCEP, and 250 mM imidazole, and concentrated by Amicon ultra centrifugal filter (Millipore, 30-kDa molecular weight cut-off) to ˜50 mg/mL. The 6×His tag and maltose-binding protein were removed by TEV protease treatment at 4° C. for 20 h and captured by a second Ni-affinity purification step. The eluent, containing Cas9, was injected into a HiTrap SP FF column (GE Healthcare) in purification buffer containing 20 mM Tris-HCl (pH 8), 0.1 M KCl, 20% glycerol, and 1 mM TCEP. Cas9 was eluted with purification buffer containing a linear KCl gradient from 0.1 M to 1 M over five column volumes. The eluted Cas9 was further purified by a HiLoad Superdex 200 column in purification buffer, snap-frozen in liquid nitrogen, and stored in aliquots at −80° C.

In Vitro RNA Transcription. 100 pmol CLTA(#) v2.1 fwd and v2.1 template rev were incubated at 95° C. and cooled at 0.1° C./s to 37° C. in NEBuffer2 (50 mM sodium chloride, 10 mM Tris-HCl, 10 mM magnesium chloride, 1 mM dithiothreitol, pH 7.9) supplemented with 10 μM dNTP mix (Bio-Rad). 10 U of Klenow Fragment (3′→5′ exo⁻) (NEB) were added to the reaction mixture and a double-stranded CLTA(#) v2.1 template was obtained by overlap extension for 1 h at 37° C. 200 nM CLTA(#) v2.1 template alone or 100 nM CLTA(#) template with 100 nM T7 promoter oligo was incubated overnight at 37° C. with 0.16 U/μL of T7 RNA Polymerase (NEB) in NEB RNAPol Buffer (40 mM Tris-HCl, pH 7.9, 6 mM magnesium chloride, 10 mM dithiothreitol, 2 mM spermidine) supplemented with 1 mM rNTP mix (1 mM rATP, 1 mM rCTP, 1 mM rGTP, 1 mM rUTP). In vitro transcribed RNA was precipitated with ethanol and purified by gel electrophoresis on a Criterion 10% polyacrylamide TBE-Urea gel (Bio-Rad). Gel-purified sgRNA was precipitated with ethanol and redissolved in water.

In Vitro Library Construction. 10 pmol of CLTA(#) lib oligonucleotides were separately circularized by incubation with 100 units of CircLigase II ssDNA Ligase (Epicentre) in 1× CircLigase II Reaction Buffer (33 mM Tris-acetate, 66 mM potassium acetate, 0.5 mM dithiothreitol, pH 7.5) supplemented with 2.5 mM manganese chloride in a total reaction volume of 20 μL for 16 hours at 60° C. The reaction mixture was incubated for 10 minutes at 85° C. to inactivate the enzyme. 5 μL (5 pmol) of the crude circular single-stranded DNA were converted into the concatemeric pre-selection libraries with the illustra TempliPhi Amplification Kit (GE Healthcare) according to the manufacturer's protocol. Concatemeric pre-selection libraries were quantified with the Quant-it PicoGreen dsDNA Assay Kit (Invitrogen).

In Vitro Cleavage of On-Target and Off-Target Substrates. Plasmid templates for PCR were constructed by ligation of annealed oligonucleotides CLTA(#) site fwd/rev into HindIII/XbaI double-digested pUC19 (NEB). On-target substrate DNAs were generated by PCR with the plasmid templates and test fwd and test rev primers, then purified with the QIAquick PCR Purification Kit (Qiagen). Off-target substrate DNAs were generated by primer extension. 100 pmol off-target (#) fwd and off-target (#) rev primers were incubated at 95° C. and cooled at 0.1° C./s to 37° C. in NEBuffer2 (50 mM sodium chloride, 10 mM Tris-HCl, 10 mM magnesium chloride, 1 mM dithiothreitol, pH 7.9) supplemented with 10 μM dNTP mix (Bio-Rad). 10 U of Klenow Fragment (3′→5′ exo-) (NEB) were added to the reaction mixture and double-stranded off-target templates were obtained by overlap extension for 1 h at 37° C. followed by enzyme inactivation for 20 min at 75° C., then purified with the QIAquick PCR Purification Kit (Qiagen). 200 nM substrate DNAs were incubated with 100 nM Cas9 and 100 nM (v1.0 or v2.1) sgRNA or 1000 nM Cas9 and 1000 nM (v1.0 or v2.1) sgRNA in Cas9 cleavage buffer (200 mM HEPES, pH 7.5, 1.5 M potassium chloride, 100 mM magnesium chloride, 1 mM EDTA, 5 mM dithiothreitol) for 10 min at 37° C. On-target cleavage reactions were purified with the QIAquick PCR Purification Kit (Qiagen), and off-target cleavage reactions were purified with the QIAquick Nucleotide Removal Kit (Qiagen) before electrophoresis in a Criterion 5% polyacrylamide TBE gel (Bio-Rad).

In Vitro Selection. 200 nM concatemeric pre-selection libraries were incubated with 100 nM Cas9 and 100 nM sgRNA or 1000 nM Cas9 and 1000 nM sgRNA in Cas9 cleavage buffer (200 mM HEPES, pH 7.5, 1.5 M potassium chloride, 100 mM magnesium chloride, 1 mM EDTA, 5 mM dithiothreitol) for 10 min at 37° C. Pre-selection libraries were also separately incubated with 2 U of BspMI restriction endonuclease (NEB) in NEBuffer 3 (100 mM NaCl, 50 mM Tris-HCl, 10 mM MgCl2, 1 mM dithiothreitol, pH 7.9) for 1 h at 37° C. Blunt-ended post-selection library members or sticky-ended pre-selection library members were purified with the QIAQuick PCR Purification Kit (Qiagen) and ligated to 10 pmol adapter1/2(AACA) (Cas9:v2.1 sgRNA, 100 nM), adapter1/2(TTCA) (Cas9:v2.1 sgRNA, 1000 nM), adapter1/2 (Cas9:v2.1 sgRNA, 1000 nM), or lib adapter1/CLTA(#) lib adapter 2 (pre-selection) with 1,000 U of T4 DNA Ligase (NEB) in NEB T4 DNA Ligase Reaction Buffer (50 mM Tris-HCl, pH 7.5, 10 mM magnesium chloride, 1 mM ATP, 10 mM dithiothreitol) overnight (>10 h) at room temperature. Adapter-ligated DNA was purified with the QIAquick PCR Purification Kit and PCR-amplified for 10-13 cycles with Phusion Hot Start Flex DNA Polymerase (NEB) in Buffer HF (NEB) and primers CLTA(#) sel PCR/PE2 short (post-selection) or CLTA(#) lib seq PCR/lib fwd PCR (pre-selection). Amplified DNAs were gel purified, quantified with the KAPA Library Quantification Kit-Illumina (KAPA Biosystems), and subjected to single-read sequencing on an Illumina MiSeq or Rapid Run single-read sequencing on an Illumina HiSeq 2500 (Harvard University FAS Center for Systems Biology Core facility, Cambridge, Mass.).

Selection Analysis. Pre-selection and post-selection sequencing data were analyzed as previously described²¹, with modification (Algorithms) using scripts written in C++. Raw sequence data is not shown; see Table 2 for a curated summary. Specificity scores were calculated with the formulae: positive specificity score=(frequency of base pair at position[post-selection]−frequency of base pair at position[pre-selection])/(1−frequency of base pair at position[pre-selection]) and negative specificity score=(frequency of base pair at position[post-selection]−frequency of base pair at position[pre-selection])/(frequency of base pair at position[pre-selection]). Normalization for sequence logos was performed as previously described²².

Cellular Cleavage Assays. HEK293T cells were split at a density of 0.8×10⁵ per well (6-well plate) before transcription and maintained in Dulbecco's modified eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS) in a 37° C. humidified incubator with 5% CO₂. After 1 day, cells were transiently transfected using Lipofectamine 2000 (Invitrogen) following the manufacturer's protocols. HEK293T cells were transfected at 70% confluency in each well of 6-well plate with 1.0 μg of the Cas9 expression plasmid (Cas9-HA-2×NLS-GFP-NLS) and 2.5 μg of the single-strand RNA expression plasmid pSiliencer-CLTA (version 1.0 or 2.1). The transfection efficiencies were estimated to be ˜70%, based on the fraction of GFP-positive cells observed by fluorescence microscopy. 48 h after transfection, cells were washed with phosphate buffered saline (PBS), pelleted and frozen at −80° C. Genomic DNA was isolated from 200 μL cell lysate using the DNeasy Blood and Tissue Kit (Qiagen) according to the manufacturer's protocol.

Off-Target Site Sequence Determination. 100 ng genomic DNA isolated from cells treated with Cas9 expression plasmid and single-strand RNA expression plasmid (treated cells) or Cas9 expression plasmid alone (control cells) were amplified by PCR with 10 s 72° C. extension for 35 cycles with primers CLTA(#)-(#)-(#) fwd and CLTA(#)-(#)-(#) rev and Phusion Hot Start Flex DNA Polymerase (NEB) in Buffer GC (NEB), supplemented with 3% DMSO. Relative amounts of crude PCR products were quantified by gel, and Cas9-treated (control) and Cas9:sgRNA-treated PCRs were separately pooled in equimolar concentrations before purification with the QIAquick PCR Purification Kit (Qiagen). Purified DNA was amplified by PCR with primers PE1-barcode# and PE2-barcode# for 7 cycles with Phusion Hot Start Flex DNA Polymerase (NEB) in Buffer HF (NEB). Amplified control and treated DNA pools were purified with the QIAquick PCR Purification Kit (Qiagen), followed by purification with Agencourt AMPure XP (Beckman Coulter). Purified control and treated DNAs were quantified with the KAPA Library Quantification Kit-Illumina (KAPA Biosystems), pooled in a 1:1 ratio, and subjected to paired-end sequencing on an Illumina MiSeq.

Statistical Analysis. Statistical analysis was performed as previously described²¹. P-values in Table 1 and Table 6 were calculated for a one-sided Fisher exact test.

Algorithms

All scripts were written in C++. Algorithms used in this study are as previous reported (reference) with modification.

Sequence binning. 1) designate sequence pairs starting with the barcode “AACA” or “TTCA” as post-selection library members. 2) for post-selection library members (with illustrated example):

-   example read:

(SEQ ID NO: 42) AACA CATGGGTCGACACAAACACAA CTCGGCAGGTACTTGCAGATGTAGT CTTTCCACATGGGTCGACACAAACACAA CTCGGCAGGTATCTCGTATGCC

-   i) search both paired reads for the positions, pos1 and pos2, of the     constant sequence

“CTCGGCAGGT”. (SEQ ID NO: 43)

-   ii) keep only sequences that have identical sequences between the     barcode and pos1 and preceding pos2. iii) keep the region between     the two instances of the constant sequence (the region between the     barcode and pos1 contains a cut half-site; the region that is     between the two instances of the constant sequence contains a full     site) -   example:

(SEQ ID NO: 44) ACTTGCAGATGTAGTCTTTCCACATGGGTCGACACAAACACAA

-   ii) search the sequence for a selection barcode

(“TGTGTTTGTGTT” (SEQ ID NO: 45) for CLTA1, “AGAAGAAGAAGA” (SEQ ID NO: 46) for CLTA2, “TTCTCTTTCTCT” (SEQ ID NO: 47) for CLTA3, “ACACAAACACAA” (SEQ ID NO: 48) for CLTA4)

-   example:

(SEQ ID NO: 49) ACTTGCAGATGTAGTCTTTCCACATGGGTCGACACAAACACAA - CLTA4

-   iii) the sequence before the barcode is the full post-selection     library member (first four and last four nucleotides are fully     randomized flanking sequence) -   example:

(SEQ ID NO: 50) ACTT GCAGATGTAGTCTTTCCACATGG GTCG

-   iv) parse the quality scores for the positions corresponding to the     23 nucleotide post-selection library member -   example read:

(SEQ ID NO: 51) AACACATGGGTCGACACAAACACAACTCGGCAGGTACTTGCAGATGTAGT CTTTCCACATGGGTCGACACAAACACAACTCGGCAGGTATCTCGTATGCC CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJGIJJJJIJIJJJIIIH IIJJJHHHGHAEFCDDDDDDDDDDDDDDDDDDDDDDD?CDDEDD@DCCCD

-   v) keep sequences only if the corresponding quality score string     (underlined) FASTQ quality characters for the sequence are ‘?’ or     higher in ASCII code (Phred quality score>=30)

NHEJ Sequence Calling

-   example read:

(SEQ ID NO: 52) CAATCTCCCGCATGCGCTCAGTCCTCATCTCCCTCAAGCAGGCCCCGCTG GTGCACTGAAGAGCCA CCCTGTGAAACACTACATCTGC AATATCTTAATC CTACTCAGTGAAGCTCTTCACAGTCATTGGATTAATTATGTTGAGTTCTT TTGGACCAAACC

-   example quality scores:

CCBCCFFFFCCCGGGGGGGGGGHHHHHHHHHHHHHHHHHHHHGGGGGGGG GHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHH HHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH HHHGHFHHHHHF

-   1) identify the 20 base pairs flanking both sides of 20 base pair     target site+three base pair PAM for each target site -   example flanking sequences:

GCTGGTGCACTGAAGAGCCA (SEQ ID NO: 53) AATATCTTAATCCTACTCAG (SEQ ID NO: 54)

-   2) search all sequence reads for the flanking sequences to identify     the potential off-target site (the sequence between the flanking     sequences) -   example potential off-target site:

CCCTGTGAAACACTACATCTGC (SEQ ID NO: 55)

-   3) if the potential off-target site contains indels (length is less     than 23), keep sequence as potential off-target site if all     corresponding FASTQ quality characters for the sequence are ‘?’ or     higher in ASCII code (Phred quality score>=30) -   example potential off-target site length=22     -   example corresponding FASTQ quality characters:         HHGHHHHHHHHHHHHHHHHHHH -   4) bin and manually inspect all sequences that pass steps 2 and 3     and keep sequences as potential modified sequences if they have at     least one deletion involving position 16, 17, or 18 (of 20 counting     from the non-PAM end) of if they have an insertion between position     17 and 18, consistent with the most frequent modifications observed     for the intended target site (FIG. 3) -   example potential off-target site (reverse complement, with     positions labeled) with reference sequence:

                     11111111112222 non-PAM end 12345678901234567890123 PAM end       GCAGATGTAGTGTTTC-ACAGGG (SEQ ID NO: 56)       GCAGATGTAGTGTTTCCACAGGG (SEQ ID NO: 57)

-   4) repeat steps 1-3 for read2 and keep only if the sequence is the     same -   5) compare overall counts in Cas9+sgRNA treated sample to Cas9 alone     sample to identify modified sites

Filter Based on Cleavage Site (for Post-Selection Sequences)

1) tabulate the cleavage site locations across the recognition site by identifying the first position in the full sequenced recognition site (between the two constant sequences) that is identical to the first position in the sequencing read after the barcode (before the first constant sequence).

2) after tabulation, repeat step 1, keeping only sequences with cleavage site locations that are present in at least 5% of the sequencing reads.

Results Broad Off-Target DNA Cleavage Profiling Reveals RNA Programmed Cas9 Nuclease Specificity.

Sequence-specific endonucleases including zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) have become important tools to modify genes in induced pluripotent stem cells (iPSCs),¹⁻³ in multi-cellular organisms,⁴⁻⁸ and in ex vivo gene therapy clinical trials.^(9, 10) Although ZFNs and TALENs have proved effective for such genetic manipulation, a new ZFN or TALEN protein must be generated for each DNA target site. In contrast, the RNA-guided Cas9 endonuclease uses RNA:DNA hybridization to determine target DNA cleavage sites, enabling a single monomeric protein to cleave, in principle, any sequence specified by the guide RNA.¹¹

Previous studies¹²⁻¹⁷ demonstrated that Cas9 mediates genome editing at sites complementary to a 20-nucleotide sequence in a bound guide RNA. In addition, target sites must include a protospacer adjacent motif (PAM) at the 3′ end adjacent to the 20-nucleotide target site; for Streptococcus pyogenes Cas9, the PAM sequence is NGG. Cas9-mediated DNA cleavage specificity both in vitro and in cells has been inferred previously based on assays against small collections of potential single-mutation off-target sites. These studies suggested that perfect complementarity between guide RNA and target DNA is required in the 7-12 base pairs adjacent to the PAM end of the target site (3′ end of the guide RNA) and mismatches are tolerated at the non-PAM end (5′ end of the guide RNA).^(11, 12, 17-19)

Although such a limited number of nucleotides specifying Cas9:guide RNA target recognition would predict multiple sites of DNA cleavage in genomes of moderate to large size (>˜10⁷ bp), Cas9:guide RNA complexes have been successfully used to modify both cells^(12, 13, 15) and organisms.¹⁴ A study using Cas9:guide RNA complexes to modify zebrafish embryos observed toxicity at a rate similar to that of ZFNs and TALENs.¹⁴ A recent, broad study of the specificity of DNA binding (transcriptional repression) in E. coli of a catalytically inactive Cas9 mutant using high-throughput sequencing found no detectable off-target transcriptional repression in the relatively small E. coli transcriptome.²⁰ While these studies have substantially advanced our basic understanding of Cas9, a systematic and comprehensive profile of Cas9:guide RNA-mediated DNA cleavage specificity generated from measurements of Cas9 cleavage on a large number of related mutant target sites has not been described. Such a specificity profile is needed to understand and improve the potential of Cas9:guide RNA complexes as research tools and future therapeutic agents.

We modified our previously published in vitro selection,²¹ adapted to process the blunt-ended cleavage products produced by Cas9 compared to the overhang-containing products of ZFN cleavage, to determine the off-target DNA cleavage profiles of Cas9:single guide RNA (sgRNA)¹¹ complexes. Each selection experiment used DNA substrate libraries containing ˜10¹² sequences, a size sufficiently large to include ten-fold coverage of all sequences with eight or fewer mutations relative to each 22-base pair target sequence (including the two-base pair PAM) (FIG. 1). We used partially randomized nucleotide mixtures at all 22 target-site base pairs to create a binomially distributed library of mutant target sites with an expected mean of 4.62 mutations per target site. In addition, target site library members were flanked by four fully randomized base pairs on each side to test for specificity patterns beyond those imposed by the canonical 20-base pair target site and PAM.

Pre-selection libraries of 10¹² individual potential off-target sites were generated for each of four different target sequences in the human clathrin light chain A (CLTA) gene (FIG. 3). Synthetic 5′-phosphorylated 53-base oligonucleotides were self-ligated into circular single-stranded DNA in vitro, then converted into concatemeric 53-base pair repeats through rolling-circle amplification. The resulting pre-selection libraries were incubated with their corresponding Cas9:sgRNA complexes. Cleaved library members containing free 5′ phosphates were separated from intact library members through the 5′ phosphate-dependent ligation of non-phosphorylated double-stranded sequencing adapters. The ligation-tagged post-selection libraries were amplified by PCR. The PCR step generated a mixture of post-selection DNA fragments containing 0.5, 1.5, or 2.5, etc. repeats of library members cleaved by Cas9, resulting from amplification of an adapter-ligated cut half-site with or without one or more adjacent corresponding full sites (FIG. 1). Post-selection library members with 1.5 target-sequence repeats were isolated by gel purification and analyzed by high-throughput sequencing. In a final computational selection step to minimize the impact of errors during DNA amplification or sequencing, only sequences with two identical copies of the repeated cut half-site were analyzed.

Pre-selection libraries were incubated under enzyme-limiting conditions (200 nM target site library, 100 nM Cas9:sgRNA v2.1) or enzyme-saturating conditions (200 nM target site library, 1000 nM Cas9:sgRNA v2.1) for each of the four guide RNAs targets tested (CLTA1, CLTA2, CLTA3, and CLTA4) (FIGS. 3C and 3D). A second guide RNA construct, sgRNA v1.0, which is less active than sgRNA v2.1, was assayed under enzyme-saturating conditions alone for each of the four guide RNA targets tested (200 nM target site library, 1000 nM Cas9:sgRNA v1.0). The two guide RNA constructs differ in their length (FIG. 3) and in their DNA cleavage activity level under the selection conditions, consistent with previous reports¹⁵ (FIG. 4). Both pre-selection and post-selection libraries were characterized by high-throughput DNA sequencing and computational analysis. As expected, library members with fewer mutations were significantly enriched in post-selection libraries relative to pre-selection libraries (FIG. 5).

Pre- and Post-Selection Library Composition. The pre-selection libraries for CLTA1, CLTA2, CLTA3, and CLTA4 had observed mean mutation rates of 4.82 (n=1,129,593), 5.06 (n=847,618), 4.66 (n=692,997), and 5.00 (n=951,503) mutations per 22-base pair target site, including the two-base pair PAM, respectively. The post-selection libraries treated under enzyme-limiting conditions with Cas9 plus CLTA1, CLTA2, CLTA3, or CLTA4 v.2.1 sgRNAs contained means of 1.14 (n=1,206,268), 1.21 (n=668,312), 0.91 (n=1,138,568), and 1.82 (n=560,758) mutations per 22-base pair target site. Under enzyme-excess conditions, the mean number of mutations among sequences surviving selection increased to 1.61 (n=640,391), 1.86 (n=399,560), 1.46 (n=936,414), and 2.24 (n=506,179) mutations per 22-base pair target site, respectively, for CLTA1, CLTA2, CLTA3, or CLTA4 v2.1 sgRNAs. These results reveal that the selection significantly enriched library members with fewer mutations for all Cas9:sgRNA complexes tested, and that enzyme-excess conditions resulted in the putative cleavage of more highly mutated library members compared with enzyme-limiting conditions (FIG. 5).

We calculated specificity scores to quantify the enrichment level of each base pair at each position in the post-selection library relative to the pre-selection library, normalized to the maximum possible enrichment of that base pair. Positive specificity scores indicate base pairs that were enriched in the post-selection library and negative specificity scores indicate base pairs that were de-enriched in the post-selection library. For example, a score of +0.5 indicates that a base pair is enriched to 50% of the maximum enrichment value, while a score of −0.5 indicates that a base pair is de-enriched to 50% of the maximum de-enrichment value.

In addition to the two base pairs specified by the PAM, all 20 base pairs targeted by the guide RNA were enriched in the sequences from the CLTA1 and CLTA2 selections (FIG. 2, FIGS. 6 and 9, and Table 2). For the CLTA3 and CLTA4 selections (FIGS. 7 and 8, and Table 2), guide RNA-specified base pairs were enriched at all positions except for the two most distal base pairs from the PAM (5′ end of the guide RNA), respectively. At these non-specified positions farthest from the PAM, at least two of the three alternate base pairs were nearly as enriched as the specified base pair. Our finding that the entire 20 base-pair target site and two base pair PAM can contribute to Cas9:sgRNA DNA cleavage specificity contrasts with the results from previous single-substrate assays suggesting that only 7-12 base pairs and two base pair PAM are specified.^(11, 12, 15)

All single-mutant pre-selection (n≧14,569) and post-selection library members (n≧103,660) were computationally analyzed to provide a selection enrichment value for every possible single-mutant sequence. The results of this analysis (FIG. 2 and FIGS. 6 and 8) show that when only single-mutant sequences are considered, the six to eight base pairs closest to the PAM are generally highly specified and the non-PAM end is poorly specified under enzyme-limiting conditions, consistent with previous findings.^(11, 12, 17-19) Under enzyme-saturating conditions, however, single mutations even in the six to eight base pairs most proximal to the PAM are tolerated, suggesting that the high specificity at the PAM end of the DNA target site can be compromised when enzyme concentrations are high relative to substrate (FIG. 2). The observation of high specificity against single mutations close to the PAM only applies to sequences with a single mutation and the selection results do not support a model in which any combination of mutations is tolerated in the region of the target site farthest from the PAM (FIG. 10-15). Analyses of pre- and post-selection library composition are described elsewhere herein, position-dependent specificity patterns are illustrated in FIGS. 18-20, PAM nucleotide specificity is illustrated in FIGS. 21-24, and more detailed effects of Cas9:sgRNA concentration on specificity are described in FIG. 2G and FIG. 25).

Specificity at the Non-PAM End of the Target Site. To assess the ability of Cas9:v2.1 sgRNA under enzyme-excess conditions to tolerate multiple mutations distal to the PAM, we calculated maximum specificity scores at each position for sequences that contained mutations only in the region of one to 12 base pairs at the end of the target site most distal from the PAM (FIG. 10-17).

The results of this analysis show no selection (maximum specificity score˜0) against sequences with up to three mutations, depending on the target site, at the end of the molecule farthest from the PAM when the rest of the sequence contains no mutations. For example, when only the three base pairs farthest from the PAM are allowed to vary (indicated by dark bars in FIG. 11C) in the CLTA2 target site, the maximum specificity scores at each of the three variable positions are close to zero, indicating that there was no selection for any of the four possible base pairs at each of the three variable positions. However, when the eight base pairs farthest from the PAM are allowed to vary (FIG. 11H), the maximum specificity scores at positions 4-8 are all greater than +0.4, indicating that the Cas9:sgRNA has a sequence preference at these positions even when the rest of the substrate contains preferred, on-target base pairs.

We also calculated the distribution of mutations (FIG. 15-17), in both pre-selection and v2.1 sgRNA-treated post-selection libraries under enzyme-excess conditions, when only the first 1-12 base pairs of the target site are allowed to vary. There is significant overlap between the pre-selection and post-selection libraries for only a subset of the data (FIG. 15-17, a-c), demonstrating minimal to no selection in the post-selection library for sequences with mutations only in the first three base pairs of the target site. These results collectively show that Cas9:sgRNA can tolerate a small number of mutations (˜one to three) at the end of the sequence farthest from the PAM when provided with maximal sgRNA:DNA interactions in the rest of the target site.

Specificity at the PAM End of the Target Site. We plotted positional specificity as the sum of the magnitudes of the specificity scores for all four base pairs at each position of each target site, normalized to the same sum for the most highly specified position (FIG. 18-20). Under both enzyme-limiting and enzyme-excess conditions, the PAM end of the target site is highly specified. Under enzyme-limiting conditions, the PAM end of the molecule is almost absolutely specified (specificity score≧+0.9 for guide RNA-specified base pairs) by CLTA1, CTLA2, and CLTA3 guide RNAs (FIG. 2 and FIG. 6-9), and highly specified by CLTA4 guide RNA (specificity score of +0.7 to +0.9). Within this region of high specificity, specific single mutations, consistent with wobble pairing between the guide RNA and target DNA, that are tolerated. For example, under enzyme-limiting conditions for single-mutant sequences, a dA:dT off-target base pair and a guide RNA-specified dG:dC base pair are equally tolerated at position 17 out of 20 (relative to the non-PAM end of the target site) of the CLTA3 target site. At this position, an rG:dT wobble RNA:DNA base pair may be formed, with minimal apparent loss of cleavage activity.

Importantly, the selection results also reveal that the choice of guide RNA hairpin affects specificity. The shorter, less-active sgRNA v1.0 constructs are more specific than the longer, more-active sgRNA v2.1 constructs when assayed under identical, enzyme-saturating conditions that reflect an excess of enzyme relative to substrate in a cellular context (FIG. 2 and FIGS. 5-8). The higher specificity of sgRNA v1.0 over sgRNA v2.1 is greater for CLTA1 and CLTA2 (˜40-90% difference) than for CLTA3 and CLTA4 (<40% difference). Interestingly, this specificity difference is localized to different regions of the target site for each target sequence (FIGS. 2H and 26). Collectively, these results indicate that different guide RNA architectures result in different DNA cleavage specificities, and that guide RNA-dependent changes in specificity do not affect all positions in the target site equally. Given the inverse relationship between Cas9:sgRNA concentration and specificity described above, we speculate that the differences in specificity between guide RNA architectures arises from differences in their overall level of DNA-cleavage activities.

Effects of Cas9:sgRNA Concentration on DNA Cleavage Specificity. To assess the effect of enzyme concentration on patterns of specificity for the four target sites tested, we calculated the concentration-dependent difference in positional specificity and compared it to the maximal possible change in positional specificity (FIG. 25). In general, specificity was higher under enzyme-limiting conditions than enzyme-excess conditions. A change from enzyme-excess to enzyme-limiting conditions generally increased the specificity at the PAM end of the target by ≧80% of the maximum possible change in specificity. Although a decrease in enzyme concentration generally induces small (˜30%) increases in specificity at the end of the target sites farthest from the PAM, concentration decreases induce much larger increases in specificity at the end of the target site nearest the PAM. For CLTA4, a decrease in enzyme concentration is accompanied by a small (˜30%) decrease in specificity at some base pairs near the end of the target site farthest from the PAM.

Specificity of PAM Nucleotides. To assess the contribution of the PAM to specificity, we calculated the abundance of all 16 possible PAM dinucleotides in the pre-selection and post-selection libraries, considering all observed post-selection target site sequences (FIG. 21) or considering only post-selection target site sequences that contained no mutations in the 20 base pairs specified by the guide RNA (FIG. 22). Considering all observed post-selection target site sequences, under enzyme-limiting conditions, GG dinucleotides represented 99.8%, 99.9%, 99.8%, and 98.5% of the post-selection PAM dinucleotides for selections with CLTA1, CLTA2, CLTA3, and CLTA4 v2.1 sgRNAs, respectively. In contrast, under enzyme-excess conditions, GG dinucleotides represented 97.7%, 98.3%, 95.7%, and 87.0% of the post-selection PAM dinucleotides for selections with CLTA1, CLTA2, CLTA3, and CLTA4 v2.1 sgRNAs, respectively. These data demonstrate that an increase in enzyme concentration leads to increased cleavage of substrates containing non-canonical PAM dinucleotides.

To account for the pre-selection library distribution of PAM dinucleotides, we calculated specificity scores for the PAM dinucleotides (FIG. 23). When only on-target post-selection sequences are considered under enzyme-excess conditions (FIG. 24), non-canonical PAM dinucleotides with a single G rather than two Gs are relatively tolerated. Under enzyme-excess conditions, Cas9:CLTA4 sgRNA 2.1 exhibited the highest tolerance of non-canonical PAM dinucleotides of all the Cas9:sgRNA combinations tested. AG and GA dinucleotides were the most tolerated, followed by GT, TG, and CG PAM dinucleotides. In selections with Cas9:CLTA1, 2, or 3 sgRNA 2.1 under enzyme-excess conditions, AG was the predominate non-canonical PAM (FIGS. 23 and 24). Our results are consistent with another recent study of PAM specificity, which shows that Cas9:sgRNA can recognize AG PAM dinucleotides²³. In addition, our results show that under enzyme-limiting conditions, GG PAM dinucleotides are highly specified, and under enzyme-excess conditions, non-canonical PAM dinucleotides containing a single G can be tolerated, depending on the guide RNA context.

To confirm that the in vitro selection results accurately reflect the cleavage behavior of Cas9 in vitro, we performed discrete cleavage assays of six CLTA4 off-target substrates containing one to three mutations in the target site. We calculated enrichment values for all sequences in the post-selection libraries for the Cas9:CLTA4 v2.1 sgRNA under enzyme-saturating conditions by dividing the abundance of each sequence in the post-selection library by the calculated abundance in the pre-selection library. Under enzyme-saturating conditions, the single one, two, and three mutation sequences with the highest enrichment values (27.5, 43.9, and 95.9) were cleaved to ≧71% completion (FIG. 27). A two-mutation sequence with an enrichment value of 1.0 was cleaved to 35%, and a two-mutation sequence with an enrichment value near zero (0.064) was not cleaved. The three-mutation sequence, which was cleaved to 77% by CLTA4 v2.1 sgRNA, was cleaved to a lower efficiency of 53% by CLTA4 v1.0 sgRNA (FIG. 28). These results indicate that the selection enrichment values of individual sequences are predictive of in vitro cleavage efficiencies.

To determine if results of the in vitro selection and in vitro cleavage assays pertain to Cas9:guide RNA activity in human cells, we identified 51 off-target sites (19 for CLTA1 and 32 for CLTA4) containing up to eight mutations that were both enriched in the in vitro selection and present in the human genome (Tables 3-5). We expressed Cas9:CLTA1 sgRNA v1.0, Cas9:CLTA1 sgRNA v2.1, Cas9:CLTA4 sgRNA v1.0, Cas9:CLTA4 sgRNA v2.1, or Cas9 without sgRNA in HEK293T cells by transient transfection and used genomic PCR and high-throughput DNA sequencing to look for evidence of Cas9:sgRNA modification at 46 of the 51 off-target sites as well as at the on-target loci; no specific amplified DNA was obtained for five of the 51 predicted off-target sites (three for CLTA1 and two for CLTA4).

Deep sequencing of genomic DNA isolated from HEK293T cells treated with Cas9:CLTA1 sgRNA or Cas9:CLTA4 sgRNA identified sequences evident of non-homologous end-joining (NHEJ) at the on-target sites and at five of the 49 tested off-target sites (CLTA1-1-1, CLTA1-2-2, CLTA4-3-1, CLTA4-3-3, and CLTA4-4-8) (Tables 1 and 6-8). The CLTA4 target site was modified by Cas9:CLTA4 v2.1 sgRNA at a frequency of 76%, while off-target sites, CLTA4-3-1 CLTA4-3-3, and CLTA4-4-8, were modified at frequencies of 24%, 0.47% and 0.73%, respectively. The CLTA1 target site was modified by Cas9:CLTA1 v2.1 sgRNA at a frequency of 0.34%, while off-target sites, CLTA1-1-1 and CLTA1-2-2, were modified at frequencies of 0.09% and 0.16%, respectively.

Under enzyme-saturating conditions with the v2.1 sgRNA, the two verified CLTA1 off-target sites, CLTA1-1-1 and CLTA1-2-2, were two of the three most highly enriched sequences identified in the in vitro selection. CLTA4-3-1 and CLTA4-3-3 were the highest and third-highest enriched sequences of the seven CLTA4 three-mutation sequences enriched in the in vitro selection that are also present in the genome. The in vitro selection enrichment values of the four-mutation sequences were not calculated, since 12 out of the 14 CLTA4 sequences in the genome containing four mutations, including CLTA4-4-8, were observed at a level of only one sequence count in the post-selection library. Taken together, these results confirm that several of the off-target substrates identified in the in vitro selection that are present in the human genome are indeed cleaved by Cas9:sgRNA complexes in human cells, and also suggest that the most highly enriched genomic off-target sequences in the selection are modified in cells to the greatest extent.

The off-target sites we identified in cells were among the most-highly enriched in our in vitro selection and contain up to four mutations relative to the intended target sites. While it is possible that heterochromatin or covalent DNA modifications could diminish the ability of a Cas9:guide RNA complex to access genomic off-target sites in cells, the identification of five out of 49 tested cellular off-target sites in this study, rather than zero or many, strongly suggests that Cas9-mediated DNA cleavage is not limited to specific targeting of only a 7-12-base pair target sequence, as suggested in recent studies.^(11, 12, 19)

The cellular genome modification data are also consistent with the increase in specificity of sgRNA v1.0 compared to sgRNA v2.1 sgRNAs observed in the in vitro selection data and discrete assays. Although the CLTA1-2-2, CLTA 4-3-3, and CLTA 4-4-8 sites were modified by the Cas9-sgRNA v2.1 complexes, no evidence of modification at any of these three sites was detected in Cas9:sgRNA v1.0-treated cells. The CLTA4-3-1 site, which was modified at 32% of the frequency of on-target CLTA4 site modification in Cas9:v2.1 sgRNA-treated cells, was modified at only 0.5% of the on-target modification frequency in v1.0 sgRNA-treated cells, representing a 62-fold change in selectivity. Taken together, these results demonstrate that guide RNA architecture can have a significant influence on Cas9 specificity in cells. Our specificity profiling findings present an important caveat to recent and ongoing efforts to improve the overall DNA modification activity of Cas9:guide RNA complexes through guide RNA engineering.^(11, 15)

Overall, the off-target DNA cleavage profiling of Cas9 and subsequent analyses show that (i) Cas9:guide RNA recognition extends to 18-20 specified target site base pairs and a two-base pair PAM for the four target sites tested; (ii) increasing Cas9:guide RNA concentrations can decrease DNA-cleaving specificity in vitro; (iii) using more active sgRNA architectures can increase DNA-cleavage specificity both in vitro and in cells but impair DNA-cleavage specificity both in vitro and in cells; and (iv) as predicted by our in vitro results, Cas9:guide RNA can modify off-target sites in cells with up to four mutations relative to the on-target site. Our findings provide key insights to our understanding of RNA-programmed Cas9 specificity, and reveal a previously unknown role for sgRNA architecture in DNA-cleavage specificity. The principles revealed in this study may also apply to Cas9-based effectors engineered to mediate functions beyond DNA cleavage.

Equivalents and Scope

Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. The scope of the present invention is not intended to be limited to the above description, but rather is as set forth in the appended claims.

In the claims articles such as “a,” “an,” and “the” may mean one or more than one unless indicated to the contrary or otherwise evident from the context. Claims or descriptions that include “or” between one or more members of a group are considered satisfied if one, more than one, or all of the group members are present in, employed in, or otherwise relevant to a given product or process unless indicated to the contrary or otherwise evident from the context. The invention includes embodiments in which exactly one member of the group is present in, employed in, or otherwise relevant to a given product or process. The invention also includes embodiments in which more than one, or all of the group members are present in, employed in, or otherwise relevant to a given product or process.

Furthermore, it is to be understood that the invention encompasses all variations, combinations, and permutations in which one or more limitations, elements, clauses, descriptive terms, etc., from one or more of the claims or from relevant portions of the description is introduced into another claim. For example, any claim that is dependent on another claim can be modified to include one or more limitations found in any other claim that is dependent on the same base claim. Furthermore, where the claims recite a composition, it is to be understood that methods of using the composition for any of the purposes disclosed herein are included, and methods of making the composition according to any of the methods of making disclosed herein or other methods known in the art are included, unless otherwise indicated or unless it would be evident to one of ordinary skill in the art that a contradiction or inconsistency would arise.

Where elements are presented as lists, e.g., in Markush group format, it is to be understood that each subgroup of the elements is also disclosed, and any element(s) can be removed from the group. It is also noted that the term “comprising” is intended to be open and permits the inclusion of additional elements or steps. It should be understood that, in general, where the invention, or aspects of the invention, is/are referred to as comprising particular elements, features, steps, etc., certain embodiments of the invention or aspects of the invention consist, or consist essentially of, such elements, features, steps, etc. For purposes of simplicity those embodiments have not been specifically set forth in haec verba herein. Thus for each embodiment of the invention that comprises one or more elements, features, steps, etc., the invention also provides embodiments that consist or consist essentially of those elements, features, steps, etc.

Where ranges are given, endpoints are included. Furthermore, it is to be understood that unless otherwise indicated or otherwise evident from the context and/or the understanding of one of ordinary skill in the art, values that are expressed as ranges can assume any specific value within the stated ranges in different embodiments of the invention, to the tenth of the unit of the lower limit of the range, unless the context clearly dictates otherwise. It is also to be understood that unless otherwise indicated or otherwise evident from the context and/or the understanding of one of ordinary skill in the art, values expressed as ranges can assume any subrange within the given range, wherein the endpoints of the subrange are expressed to the same degree of accuracy as the tenth of the unit of the lower limit of the range.

In addition, it is to be understood that any particular embodiment of the present invention may be explicitly excluded from any one or more of the claims. Where ranges are given, any value within the range may explicitly be excluded from any one or more of the claims. Any embodiment, element, feature, application, or aspect of the compositions and/or methods of the invention, can be excluded from any one or more claims. For purposes of brevity, all of the embodiments in which one or more elements, features, purposes, or aspects is excluded are not set forth explicitly herein.

Tables

Table 1. Cellular modification induced by Cas9:CLTA4 sgRNA. 33 human genomic DNA sequences were identified that were enriched in the Cas9:CLTA4 v2.1 sgRNA in vitro selections under enzyme-limiting or enzyme-saturating conditions. Sites shown with underline contain insertions or deletions (indels) that are consistent with significant Cas9:sgRNA-mediated modification in HEK293T cells. In vitro enrichment values for selections with Cas9:CLTA4 v1.0 sgRNA or Cas9:CLTA4 v2.1 sgRNA are shown for sequences with three or fewer mutations. Enrichment values were not calculated for sequences with four or more mutations due to low numbers of in vitro selection sequence counts. Modification frequencies (number of sequences with indels divided by total number of sequences) in HEK293T cells treated with Cas9 without sgRNA (“no sgRNA”), Cas9 with CLTA4 v1.0 sgRNA, or Cas9 with CLTA4 v2.1 sgRNA. P-values are listed for those sites that show significant modification in v1.0 sgRNA- or v2.1 sgRNA-treated cells compared to cells treated with Cas9 without sgRNA. “Not tested (n.t.)” indicates that PCR of the genomic sequence failed to provide specific amplification products.

Table 2: Raw selection sequence counts. Positions −4 to −1 are the four nucleotides preceding the 20-base pair target site. PAM1, PAM2, and PAM3 are the PAM positions immediately following the target site. Positions +4 to +7 are the four nucleotides immediately following the PAM.

Table 3: CLTA1 genomic off-target sequences. 20 human genomic DNA sequences were identified that were enriched in the Cas9:CLTA1 v2.1 sgRNA in vitro selections under enzyme-limiting or enzyme-excess conditions. “m” refers to number of mutations from on-target sequence with mutations shown in lower case. Sites shown with underline contain insertions or deletions (indels) that are consistent with significant Cas9:sgRNA-mediated modification in HEK293T cells. Human genome coordinates are shown for each site (assembly GRCh37). CLTA1-0-1 is present at two loci, and sequence counts were pooled from both loci. Sequence counts are shown for amplified and sequenced DNA for each site from HEK293T cells treated with Cas9 without sgRNA (“no sgRNA”), Cas9 with CLTA1 v1.0 sgRNA, or Cas9 with CLTA1 v2.1 sgRNA.

Table 4: CLTA4 genomic off-target sequences. 33 human genomic DNA sequences were identified that were enriched in the Cas9:CLTA4 v2.1 sgRNA in vitro selections under enzyme-limiting or enzyme-excess conditions. “m” refers to number of mutations from on-target sequence with mutations shown in lower case. Sites shown with underline contain insertions or deletions (indels) that are consistent with significant Cas9:sgRNA-mediated modification in HEK293T cells. Human genome coordinates are shown for each site (assembly GRCh37). Sequence counts are shown for amplified and sequenced DNA for each site from HEK293T cells treated with Cas9 without sgRNA (“no sgRNA”), Cas9 with CLTA4 v1.0 sgRNA, or Cas9 with CLTA4 v2.1 sgRNA.

Table 5: Genomic coordinates of CLTA1 and CLTA4 off-target sites. 54 human genomic DNA sequences were identified that were enriched in the Cas9:CLTA1 v2.1 sgRNA and Cas9: CLTA4 v2.1 sgRNA in vitro selections under enzyme-limiting or enzyme-excess conditions. Human genome coordinates are shown for each site (assembly GRCh37).

Table 6: Cellular modification induced by Cas9:CLTA1 sgRNA. 20 human genomic DNA sequences were identified that were enriched in the Cas9:CLTA1 v2.1 sgRNA in vitro selections under enzyme-limiting or enzyme-excess conditions. Sites shown with underline contain insertions or deletions (indels) that are consistent with significant Cas9:sgRNA-mediated modification in HEK293T cells. In vitro enrichment values for selections with Cas9:CLTA1 v1.0 sgRNA or Cas9:CLTA1 v2.1 sgRNA are shown for sequences with three or fewer mutations. Enrichment values were not calculated for sequences with four or more mutations due to low numbers of in vitro selection sequence counts. Modification frequencies (number of sequences with indels divided by total number of sequences) in HEK293T cells treated with Cas9 without sgRNA (“no sgRNA”), Cas9 with CLTA1 v1.0 sgRNA, or Cas9 with CLTA1 v2.1 sgRNA. P-values of sites that show significant modification in v1.0 sgRNA- or v2.1 sgRNA-treated cells compared to cells treated with Cas9 without sgRNA were 1.1E−05 (v1.0) and 6.9E−55 (v2.1) for CLTA1-0-1, 2.6E−03 (v1.0) and 2.0E−10 (v2.1) for CLTA1-1-1, and 4.6E−08 (v2.1) for CLTA1-2-2. P-values were calculated using a one-sided Fisher exact test. “Not tested (n.t.)” indicates that the site was not tested or PCR of the genomic sequence failed to provide specific amplification products.

Table 7: CLTA1 genomic off-target indel sequences. Insertion and deletion-containing sequences from cells treated with amplified and sequenced DNA for the on-target genomic sequence (CLTA1-0-1) and each modified off-target site from HEK293T cells treated with Cas9 without sgRNA (“no sgRNA”), Cas9 with CLTA1 v1.0 sgRNA, or Cas9 with CLTA1 v2.1 sgRNA. “ref” refers to the human genome reference sequence for each site, and the modified sites are listed below. Mutations relative to the on-target genomic sequence are shown in lowercase letters. Insertions and deletions are shown in underlined bold letters or dashes, respectively. Modification percentages are shown for those conditions (v1.0 sgRNA or v2.1 sgRNA) that show statistically significant enrichment of modified sequences compared to the control (no sgRNA).

Table 8: CLTA4 genomic off-target indel sequences. Insertion and deletion-containing sequences from cells treated with amplified and sequenced DNA for the on-target genomic sequence (CLTA4-0-1) and each modified off-target site from HEK293T cells treated with Cas9 without sgRNA (“no sgRNA”), Cas9 with CLTA4 v1.0 sgRNA, or Cas9 with CLTA4 v2.1 sgRNA. “ref” refers to the human genome reference sequence for each site, and the modified sites are listed below. Mutations relative to the on-target genomic sequence are shown in lowercase letters. Insertions and deletions are shown in underlined bold letters or dashes, respectively. Modification percentages are shown for those conditions (v1.0 sgRNA or v2.1 sgRNA) that show statistically significant enrichment of modified sequences compared to the control (no sgRNA).

Table 9: Oligonucleotides used in this study. All oligonucleotides were purchased from Integrated DNA Technologies. An asterisk (*) indicates that the preceding nucleotide was incorporated as a hand mix of phosphoramidites consisting of 79 mol % of the phosphoramidite corresponding to the preceding nucleotide and 4 mol % of each of the other three canonical phosphoramidites. “/5Phos/” denotes a 5′ phosphate group installed during synthesis.

TABLE 1 # of Mutations sequence SEQ ID NO. gene CLTA4-0-1 0 GCAGATGTAGTGTTTCCACAGGG SEQ ID NO: 58 CLTA CLTA4-3-1 3 aCAtATGTAGTaTTTCCACAGGG SEQ ID NO: 59 CLTA4-3-2 3 GCAtATGTAGTGTTTCCAaATGt SEQ ID NO: 60 CLTA4-3-3 3 cCAGATGTAGTaTTcCCACAGGG SEQ ID NO: 61 CELF1 CLTA4-3-4 3 GCAGtTtTAGTGTTTtCACAGGG SEQ ID NO: 62 BC073807 CLTA4-3-5 3 GCAGAgtTAGTGTTTCCACACaG SEQ ID NO: 63 MPPED2 CLTA4-3-6 3 GCAGATGgAGgGTTTtCACAGGG SEQ ID NO: 64 DCHS2 CLTA4-3-7 3 GgAaATtTAGTGTTTCCACAGGG SEQ ID NO: 65 CLTA4-4-1 4 aaAGAaGTAGTaTTTCCACATGG SEQ ID NO: 66 CLTA4-4-2 4 aaAGATGTAGTcaTTCCACAAGG SEQ ID NO: 67 CLTA4-4-3 4 aaAtATGTAGTcTTTCCACAGGG SEQ ID NO: 68 CLTA4-4-4 4 atAGATGTAGTGTTTCCAaAGGa SEQ ID NO: 69 NR1H4 CLTA4-4-5 4 cCAGAgGTAGTGcTcCCACAGGG SEQ ID NO: 70 CLTA4-4-6 4 cCAGATGTgagGTTTCCACAAGG SEQ ID NO: 71 XKR6 CLTA4-4-7 4 ctAcATGTAGTGTTTCCAtATGG SEQ ID NO: 72 HKR1 CLTA4-4-8 4 ctAGATGaAGTGcTTCCACATGG SEQ ID NO: 73 CDK8 CLTA4-4-9 4 GaAaATGgAGTGTTTaCACATGG SEQ ID NO: 74 CLTA4-4-10 4 GCAaATGaAGTGTcaCCACAAGG SEQ ID NO: 75 CLTA4-4-11 4 GCAaATGTAtTaTTTCCACtAGG SEQ ID NO: 76 NOV CLTA4-4-12 4 GCAGATGTAGctTTTgtACATGG SEQ ID NO: 77 CLTA4-4-13 4 GCAGcTtaAGTGTTTtCACATGG SEQ ID NO: 78 GRHL2 CLTA4-4-14 4 ttAcATGTAGTGTTTaCACACGG SEQ ID NO: 79 LINC00535 CLTA4-5-1 5 GaAGAgGaAGTGTTTgCcCAGGG SEQ ID NO: 80 RNH1 CLTA4-5-2 5 GaAGATGTgGaGTTgaCACATGG SEQ ID NO: 81 FZD3 CLTA4-5-3 5 GCAGAaGTAcTGTTgttACAAGG SEQ ID NO: 82 CLTA4-5-4 5 GCAGATGTgGaaTTaCaACAGGG SEQ ID NO: 83 SLC9A2 CLTA4-5-5 5 GCAGtcaTAGTGTaTaCACATGG SEQ ID NO: 84 CLTA4-5-6 5 taAGATGTAGTaTTTCCAaAAGt SEQ ID NO: 85 CLTA4-6-1 6 GCAGcTGgcaTtTcTCCACACGG SEQ ID NO: 86 CLTA4-6-2 6 GgAGATcTgaTGgTTCtACAAGG SEQ ID NO: 87 CLTA4-6-3 6 taAaATGcAGTGTaTCCAtATGG SEQ ID NO: 88 SMA4 CLTA4-7-1 7 GCcagaaTAGTtTTTCaACAAGG SEQ ID NO: 89 SEPHS2 CLTA4-7-2 8 ttgtATtTAGaGaTTgCACAAGG SEQ ID NO: 90 RORB modification in vitro frequency in enrichment HEK293T cells P-value v1.0 v2.1 no sgRNA v1.0 v2.1 v1.0 v2.1 CLTA4-0-1 20     7.95 0.021%   11%    76%  <1E−55 <1E−55 CLTA4-3-1 16.5   12.5   0.006% 0.055%     24% 6.0E−0 <1E−55 CLTA4-3-2 2.99 6.97 0.017%    0% 0.014% CLTA4-3-3 1.00 4.95     0%    0% 0.469% 2.5E−21  CLTA4-3-4 0.79 3.12     0%    0%     0% CLTA4-3-5 0    1.22 0.005% 0.015%  0.018% CLTA4-3-6 1.57 1.17 0.015% 0.023%  0.021% CLTA4-3-7 0.43 0.42 0.005% 0.012%  0.003% CLTA4-4-1 n.t. n.t. n.t. CLTA4-4-2 0.004%    0% 0.005% CLTA4-4-3 0.004% 0.009%      0% CLTA4-4-4 0.032% 0.006%  0.052% CLTA4-4-5 0.005% 0.006%  0.007% CLTA4-4-6 0.018%    0% 0.007% CLTA4-4-7 0.006%    0% 0.008% CLTA4-4-8 0.009% 0.013%  0.730% 9.70E−21   CLTA4-4-9     0%    0% 0.004% CLTA4-4-10 0.004%    0%     0% CLTA4-4-11     0% 0.00%     0% CLTA4-4-12     0% 0.00%     0% CLTA4-4-13 0.020% 0.02% 0.030% CLTA4-4-14 n.t. n.t. n.t. CLTA4-5-1 0.004% 0.01% 0.006% CLTA4-5-2 0.004% 0.00%    0% CLTA4-5-3 0.002% 0.00% 0.003% CLTA4-5-4     0% 0.00%     0% CLTA4-5-5 0.004% 0.00% 0.005% CLTA4-5-6 0.007% 0.01%     0% CLTA4-6-1 n.t. n.t. n.t. CLTA4-6-2 0.007% 0.00% 0.009% CLTA4-6-3 0.015% 0.00%     0% CLTA4-7-1     0% 0.00% 0.007% CLTA4-7-2     0% 0.00%     0%

TABLE 2 position −4 −3 −2 −1 1 2 3 4 5 6 7 100 nM Cas9:CLTA1 v2.1 sgRNA A 212906 240335 195549 240068 1.04E+06 72751 40206 62972 41734 17376 18710 C 285295 248395 263973 260202 37925 32496 24822 1.10E+06 1.12E+06 42444 1.16E+06 G 214213 219078 220275 189578 61062 1.04E+06 25785 11117 9125 5423 5745 T 493854 498460 526471 516420 64694 59173 1.12E+06 35336 34236 1.14E+06 20532 1000 nM Cas9:CLTA1 v1.0 sgRNA A 154613 184336 154288 177436 805105 66777 43354 56461 32941 15531 19465 C 227144 201856 215667 220894 30269 30133 24249 825333 865486 35164 889622 G 163868 174062 177891 148150 47940 784264 26342 17972 10299 6332 5785 T 389059 374430 386838 388204 51370 53510 840739 34918 25958 877657 19812 1000 nM Cas9:CLTA1 v2.1 sgRNA A 104782 127116 103361 124521 554601 40232 29541 38710 23659 10435 11462 C 154144 136337 145670 146754 20057 19440 17922 569754 590426 25233 612203 G 113998 119668 120741 103026 32861 547445 18468 9314 6346 3908 4295 T 267467 257270 270619 266090 32872 33274 574460 22613 19960 600815 12431 CLTA1 pre-selection library A 241543 217144 209045 198284 943175 103452 76259 106919 124476 59762 108373 C 254366 269805 276090 322860 52984 65855 58943 834238 812029 52168 839963 G 230024 196574 210445 180859 60496 857631 66783 89366 85315 67098 77499 T 403590 446000 433943 427520 72868 102585 927538 99000 107703 950495 103688 100 nM Cas9:CLTA2 v2.1 sgRNA A 109129 135587 94032 141748 5.74E+04 44902 48284 24464 11611 16668 6282 C 155710 138970 207735 220443 529643 24503 566049 6.27E+05 6.46E+05 19040 6.52E+05 G 136555 142038 118241 105620 39991 2.11E+04 26481 3756 3627 2889 2488 T 266918 251717 248304 200501 41277 577893 2.75E+04 13008 7318 6.30E+05 7487 1000 nM Cas9:CLTA2 v1.0 sgRNA A 94138 115828 85485 120876 52411 41438 46093 22399 9068 14310 5351 C 140895 125708 179224 191394 452192 21517 481298 538392 557549 16233 562576 G 113243 118054 101838 91048 35101 18969 22797 3440 2802 2960 2526 T 228367 217053 209898 173125 38739 494519 26255 12212 7026 542940 5990 1000 nM Cas9:CLTA2 v2.1 sgRNA A 64249 81812 58977 65387 35172 29833 33434 19419 9272 13136 4907 C 96983 87918 124642 187760 316077 14548 327166 364874 380987 11360 387025 G 77913 80500 68612 64299 23522 15749 19664 3856 3035 2752 2062 T 160415 149330 147329 122114 94789 339431 19296 11411 6266 372312 5566 CLTA2 pre-selection library A 203147 173899 167999 170203 89970 73770 88239 88611 76114 78589 75016 C 181430 214835 246369 272618 632831 41977 641062 644565 670872 40877 649838 G 177090 153006 151178 140868 68664 49976 60827 56077 52341 49259 55484 T 285951 305878 282072 263929 66153 881895 57490 58365 48291 678892 67280 100 nM Cas9:CLTA3 v2.1 sgRNA A 212836 248582 202151 249368 9.13E+04 77392 19048 39738 1078580 1106930 46196 C 233270 241259 274819 305120 37894 35918 13930 5.61E+03 1.22E+04 3774 6.35E+03 G 211701 187534 185231 196614 66632 9.88E+05 26572 1074020 12936 9205 1066570 T 480761 461193 476317 387466 342707 37284 1.09E+05 19204 34885 1.87E+04 19450 1000 nM Cas9:CLTA3 v1.0 sgRNA A 219823 263464 207913 264018 97886 78562 20562 29724 1126320 1151200 42366 C 240570 261247 311444 333414 39996 40484 13261 5323 11093 5475 10323 G 221683 206195 199246 215583 76580 1032080 24785 1126840 12654 12465 1114450 T 506611 457791 470094 375682 974235 37571 1129290 16811 28626 19580 20956 1000 nM Cas9:CLTA3 v2.1 sgRNA A 169775 206549 166197 201768 75243 67150 20443 36549 876154 838360 39901 C 197800 203445 243688 264177 32775 34540 14250 7885 14793 4378 7791 G 174766 158928 153884 168325 58121 801763 26558 356689 13343 12052 368394 T 394073 361492 367705 302144 770275 32956 875157 25291 32124 21124 20328 CLTA3 pre-selection library A 173122 135327 133244 142593 50365 69485 37040 56315 575295 566722 70243 C 143788 158534 162046 177240 25902 40142 28129 34669 38933 36129 61591 G 137601 132826 130592 128304 42860 534378 42217 531723 29873 34068 479149 T 238486 266310 261515 244854 573870 48391 595611 60291 48596 56079 82008 100 nM Cas9:CLTA4 v2.1 sgRNA A 55030 78101 78867 81833 8.09E+04 58148 525585 29962 544918 19446 54151 C 168401 162082 139480 130495 22088 428628 4498 1.21E+04 5.14E+03 15601 7.10E+03 G 89302 75785 82959 133275 415632 4.70E+04 14868 504358 6156 9951 493432 T 248025 244790 259452 215155 42090 26956 1.58E+04 14300 4541 5.16E+05 6071 1000 nM Cas9:CLTA4 v1.0 sgRNA A 95188 141261 145156 141850 151224 116745 928773 50295 975924 29201 95476 C 305024 297215 260676 243819 34420 745345 8606 17266 7541 29948 10779 G 159888 139073 153474 225343 742232 85777 29776 907007 9285 13455 883325 T 438973 421524 439767 388061 71197 51206 31918 24505 6323 926469 9493 1000 nM Cas9:CLTA4 v2.1 sgRNA A 47674 70467 71535 72698 72554 54587 471218 27627 493315 16818 47470 C 154985 151636 133622 122579 18730 384037 4452 10916 4303 16232 5436 G 80869 69972 76726 118084 379024 42360 14989 453870 5084 6863 448784 T 222651 214104 224296 192818 35871 25195 15520 13766 3477 466266 4489 CLTA4 pre-selection library A 106798 131577 131941 132368 127160 103294 820923 103844 840417 99163 133349 C 304597 297419 277233 283453 50833 722264 29748 65558 44890 59551 73916 G 146240 137027 134399 183111 695802 68240 51484 708098 30709 62837 673752 T 393868 385480 407930 352571 77708 57705 49348 74003 35487 729952 70486 position 8 9 10 11 12 13 14 15 16 17 100 nM Cas9:CLTA1 v2.1 sgRNA A 1.17E+06 24455 83195 46083 33528 8551 9668 4582 32237 1.19E+06 C 5339 22096 1.06E+06 48105 1.14E+06 1.14E+06 1.18E+06 4090 1.13E+06 4363 G 5121 8080 14905 8906 3732 3294 3867 3597 7260 3400 T 24018 1.15E+06 50488 1.10E+06 32417 57980 13065 1.19E+06 36826 8959 1000 nM Cas9:CLTA1 v1.0 sgRNA A 904223 19696 56566 35200 26674 7925 9269 4859 32891 910633 C 5488 17340 828521 36975 876790 880022 908816 4419 859691 5694 G 5938 9185 11560 10641 3020 2819 3185 2994 6763 3631 T 19035 888463 38037 851868 28200 43918 13414 922412 35339 14726 1000 nM Cas9:CLTA1 v2.1 sgRNA A 618404 14608 41826 27762 19590 8961 19434 9549 35083 604115 C 3834 15297 561351 26392 592757 594469 616112 11645 553993 13212 G 3719 5851 10887 15360 5605 3378 3517 5896 22551 8658 T 14434 604635 26327 570877 22439 33583 1328 613301 28764 14406 CLTA1 pre-selection library A 937511 65477 110282 67774 96299 88029 109977 62686 119399 931093 C 54708 43285 831610 50109 861358 841819 817157 51676 797914 60106 G 59257 71824 89579 68090 66121 86080 96496 81367 104949 52143 T 78047 948937 98052 943550 105745 113595 105893 933794 107261 86181 100 nM Cas9:CLTA2 v2.1 sgRNA A 6.58E+05 655917 28909 24210 656617 59160 36601 2974 12980 3.27E+03 C 2951 2577 1.30E+04 617274 2.64E+03 1.48E+04 9.12E+03 660929 6.50E+05 660305 G 3025 3202 609865 8312 5889 581322 606454 1564 2134 1819 T 4920 6.62E+03 16554 1.85E+04 3165 13024 16134 2.85E+03 3253 2918 1000 nM Cas9:CLTA2 v1.0 sgRNA A 567337 565061 24132 23848 558483 49577 39401 5428 30774 6408 C 1973 2127 11807 525901 4892 13617 13316 563557 535780 560658 G 2895 2793 526655 9738 8100 495156 496382 1789 3325 1846 T 4238 6462 13849 16956 4868 18093 27344 5672 6564 7531 1000 nM Cas9:CLTA2 v2.1 sgRNA A 391675 389930 13852 16657 383605 32780 22855 9722 25181 12518 C 1694 1815 8124 363374 5168 9569 9710 374342 355544 373485 G 2398 2439 360755 7431 6019 344511 350245 1559 5882 1339 T 3793 5376 10829 12098 4768 12700 16750 13937 12953 12819 CLTA2 pre-selection library A 726091 712150 96111 90307 728931 91515 84764 79586 86205 87337 C 38931 44691 46591 628706 32296 49519 46571 641958 624548 637703 G 39801 38939 630670 55013 38368 627263 642878 59549 55292 53066 T 42795 51838 74246 73592 48023 79321 73405 66528 81573 69522 100 nM Cas9:CLTA3 v2.1 sgRNA A 1.12E+06 64461 11912 30992 21158 6465 1130430 4037 5750 4.71E+04 C 4063 6018 1.11E+06 27501 4.68E+04 1.12E+06 1.96E+03 1123400 1.82E+03 3421 G 7418 1050360 3828 3949 2231 2504 2471 1726 2881 1081680 T 11145 1.77E+04 13689 1.08E+06 1068370 3829 3709 3.34E+03 1128120 6398 1000 nM Cas9:CLTA3 v1.0 sgRNA A 1156400 49443 18669 44652 44644 44771 1152540 16264 30980 71714 C 6501 8456 1126310 36792 56203 1086280 8427 1156840 8448 25120 G 12075 1112930 12078 19275 9014 7707 9466 2708 17195 1053760 T 13723 16864 31636 1087980 1078840 39940 16250 12883 1132070 38102 1000 nM Cas9:CLTA3 v2.1 sgRNA A 911344 44415 13218 37301 33080 26409 893670 6315 20807 52541 C 4636 7510 390531 28425 46269 870864 7991 310584 5931 19923 G 8637 667980 7923 14022 6553 3893 7912 1499 12906 836022 T 11597 16509 24682 856666 850512 35749 26841 16016 896770 27928 CLTA3 pre-selection library A 528947 72610 41265 61770 56547 75555 586476 61203 51740 70943 C 52201 46032 559715 32233 34830 519328 30904 540977 24982 45344 G 49753 501888 41949 43243 30118 38922 34282 34082 37275 515778 T 82036 72467 50068 555751 571502 59192 41335 56735 579000 60932 100 nM Cas9:CLTA4 v2.1 sgRNA A 2.59E+04 550200 29521 34194 38891 26542 23991 15243 25122 5.36E+03 C 35217 2481 2.35E+04 16846 2.03E+04 3.69E+04 8.47E+03 5182 5.22E+05 547711 G 14899 4528 498832 27411 497382 6729 3344 3716 3926 3162 T 484788 3.55E+03 8877 4.82E+05 4222 490573 524958 5.37E+05 9437 4528 1000 nM Cas9:CLTA4 v1.0 sgRNA A 30383 980248 50181 65094 77253 42674 41050 32933 55244 39984 C 47831 5069 32501 30389 29610 61641 25910 21400 887446 900777 G 19640 8303 902733 44730 879985 16677 7879 8429 12432 17373 T 901219 5453 13658 858860 12225 878081 924234 936311 43951 40939 1000 nM Cas9:CLTA4 v2.1 sgRNA A 17728 498471 29769 40021 41618 24741 23050 16409 27974 2697 C 28594 1961 19017 19152 18001 35213 12845 13497 445302 480543 G 10260 3281 450120 23076 439828 7741 5091 5456 7558 7112 T 449597 2466 7273 423930 6732 438484 465193 470817 25345 15827 CLTA4 pre-selection library A 123366 824537 126564 115133 122618 108492 107761 96384 99908 76163 C 77470 45318 84973 73106 90384 78280 76978 66776 738550 776738 G 89897 49093 672860 88125 663922 67768 53472 58440 47550 41427 T 660770 32555 67106 675139 74579 696963 713292 729903 65495 57175 position 18 19 20 PAM1 PAM2 PAM3 +4 +5 +6 +7 100 nM Cas9:CLTA1 v2.1 sgRNA A 1.20E+06 2032 4237 261056 1386 574 235167 223887 222343 301356 C 628 969 1.19E+06 210095 167 152 211027 273777 264354 309690 G 2474 1.19E+06 1301 238989 1.20E+06 1.21E+06 205765 222282 240526 217260 T 3966 9354 8065 496128 475 211 554303 486322 479045 377362 1000 nM Cas9:CLTA1 v1.0 sgRNA A 925527 3595 5976 183479 1390 413 182704 171051 174062 221899 C 776 2120 920211 180463 120 88 180657 220438 211411 245967 G 2894 916417 1415 193418 932808 934044 172551 172071 176484 161703 T 5487 12552 7082 377324 366 139 398772 371124 372727 305115 1000 nM Cas9:CLTA1 v2.1 sgRNA A 607264 4665 16515 125225 10391 2519 125288 114575 120476 149847 C 4438 5146 590160 116022 329 138 123802 154249 146572 166531 G 12770 613580 3712 121392 628464 637588 118800 113560 118464 111278 T 15919 17000 30004 277752 1207 146 272501 258007 254879 212735 CLTA1 pre-selection library A 908362 64248 111479 190574 97896 104002 183367 178912 198049 219754 C 52998 42317 813253 239201 56843 59450 289074 295400 289007 284268 G 77389 918970 96000 192652 879150 870948 196672 202194 196499 202544 T 90774 103988 108791 507096 95634 95123 460410 453017 445968 422957 100 nM Cas9:CLTA2 v2.1 sgRNA A 1.09E+03 17686 689 193742 284 129 143150 165553 136708 146056 C 666122 1314 6.65E+05 42664 48 43 162563 111729 143442 177253 G 89 6.44E+05 505 137388 6.68E+05 6.68E+05 103305 146355 139972 124772 T 1016 4886 2608 294518 146 48 259294 244675 248190 220231 1000 nM Cas9:CLTA2 v1.0 sgRNA A 5055 36081 2573 148145 782 243 132801 126862 118528 122897 C 567693 4938 569653 46472 70 45 133402 123970 130555 148756 G 166 519782 520 125177 575395 576103 118877 108849 104210 103370 T 3529 15642 3697 256649 196 52 191363 216762 223150 201420 1000 nM Cas9:CLTA2 v2.1 sgRNA A 17950 28198 5471 100745 4933 834 89339 87351 82615 85108 C 370343 11652 378841 40532 238 34 93621 87320 91380 105625 G 391 331376 1034 74803 393760 398660 79776 75927 74068 70435 T 10876 28334 14214 183480 629 32 136824 148362 151497 138392 CLTA2 pre-selection library A 85547 92983 100316 177716 84144 88017 177831 180209 176904 174190 C 635473 51727 594349 136372 41282 41689 216880 206368 210039 235263 G 57979 616575 66553 158929 656315 654970 162242 160704 157741 138890 T 68619 86333 86400 274601 65877 62942 290665 300337 302934 299275 100 nM Cas9:CLTA3 v2.1 sgRNA A 1.14E+06 6151 2047 305062 1993 394 213566 240851 230230 252637 C 167 1451 6.66E+02 261609 103 82 313990 253055 261338 293644 G 876 1.13E+06 600 228865 1.14E+06 1.14E+06 142425 192720 220683 237840 T 1320 4480 1135260 343032 211 69 462587 451942 426317 364447 1000 nM Cas9:CLTA3 v1.0 sgRNA A 1156700 47106 27658 276285 26304 12701 219034 239515 244440 255260 C 4351 24685 9473 297135 1331 939 354289 298216 277740 292917 G 10278 1085310 10308 238545 1148550 1174510 171862 193096 217301 239319 T 17372 31596 1141260 376732 2514 560 443512 457870 449216 401101 1000 nM Cas9:CLTA3 v2.1 sgRNA A 903619 33690 20904 205940 26623 9880 172210 182986 187305 196429 C 4977 16171 6508 223797 1163 693 283240 240802 224453 236469 G 9011 859600 8302 190011 906628 925513 132620 153591 172169 167623 T 18807 24953 900700 310666 2000 323 346344 359035 352487 315893 CLTA3 pre-selection library A 563277 70484 50807 130402 57527 61702 110207 118993 126967 127707 C 35359 44014 35778 174938 42259 46083 201434 190347 184768 207347 G 36956 516177 45203 137307 539445 527404 113323 119846 118423 127230 T 51405 62322 561209 250350 53766 57808 268033 263811 262839 230713 100 nM Cas9:CLTA4 v2.1 sgRNA A 5.51E+05 1994 540029 47731 4642 1401 77633 56902 63224 54815 C 5715 546119 3.02E+03 152056 655 473 141123 164035 146401 190955 G 554 1.45E+03 4637 72296 5.55E+05 5.58E+05 84257 77627 75123 91454 T 3692 11194 13069 288675 911 495 257745 262194 276010 223534 1000 nM Cas9:CLTA4 v1.0 sgRNA A 942989 19900 887311 80159 28536 12390 142460 96664 110844 99920 C 34590 940504 23749 257985 2556 4791 252462 297152 258929 338099 G 4103 7346 20095 139488 964013 976818 154302 139784 136512 165750 T 17391 31323 67918 521441 3968 5074 449849 465473 492788 395304 1000 nM Cas9:CLTA4 v2.1 sgRNA A 478335 12667 451298 36128 22041 16967 68943 49017 56451 51102 C 15631 469503 11832 122541 3529 8965 126313 153105 134293 171499 G 3083 5302 10184 87517 474540 471647 85849 72063 71600 85239 T 9130 18707 32865 259993 6069 8600 225074 231994 243835 198339 CLTA4 pre-selection library A 806675 75877 793806 87755 82113 83605 111015 103082 109315 101198 C 55522 754283 42188 278802 57603 55530 266156 281433 258029 295144 G 42574 54424 59162 151536 740525 732891 163824 158224 146268 151560 T 46732 66919 56347 433410 71265 79477 410508 408764 437891 403601

TABLE 3 no sgRNA v1.0 sgRNA v2.1 sgRNA modified total modified total modified total m sequence sequences sequences sequences sequences sequences sequences CLTA1-0- 0 AGTCCTCATCTCCCTCAAGCAGG 2 58889 18  42683 178   52845 (SEQ ID NO: 91) CLTA1-1-1 1 AGTCCTCAaCTCCCTCAAGCAGG 1 39804 9 29000 37  40588 (SEQ ID NO: 92) CLTA1-2-1 2 AGcCCTCATtTCCCTCAAGCAGG 0 16276 0 15032 0 18277 (SEQ ID NO: 93) CLTA1-2-2 2 AcTCCTCATCcCCCTCAAGCCGG 3 21267 1 20042 33  22579 (SEQ ID NO: 94) CLTA1-2-3 2 AGTCaTCATCTCCCTCAAGCAGa 0     0 0     0 0     0 (SEQ ID NO: 95) CLTA1-3-1 3 cGTCCTCcTCTCCCcCAAGCAGG 2 53901 0 42194 0 52205 (SEQ ID NO: 96) CLTA1-3-2 3 tGTCCTCtTCTCCCTCAAGCAGa 0 14890 0 14231 0 15937 (SEQ ID NO: 97) CLTA1-4-1 4 AagCtTCATCTCtCTCAAGCTGG 0 49579 2 31413 0 41234 (SEQ ID NO: 98) CLTA1-4-2 4 AGTaCTCtTtTCCCTCAgGCTGG 2 30013 1 23470 4 26999 (SEQ ID NO: 99) CLTA1-4-3 4 AGTCtTaAatTCCCTCAAGCAGG 2 63792 0 52321 1 73007 (SEQ ID NO: 100) CLTA1-4-4 4 AGTgCTCATCTaCCagAAGCTGG 1 12585 0 11339 0 12066 (SEQ ID NO: 101) CLTA1-4-5 4 ccTCCTCATCTCCCTgcAGCAGG 4 30568 1 23810 0 27870 (SEQ ID NO: 102) CLTA1-4-6 4 ctaCaTCATCTCCCTCAAGCTGG 0 13200 1 12886 2 12843 (SEQ ID NO: 103) CLTA1-4-7 4 gGTCCTCATCTCCCTaAAaCAGa 1  8697 3  8188 0  8783 (SEQ ID NO: 104) CLTA1-4-8 4 tGTCCTCATCggCCTCAgGCAGG 0 13169 0  8805 2 12830 (SEQ ID NO: 105) CLTA1-5-1 5 AGaCacCATCTCCCTtgAGCTGG 0 46109 1 32515 2 35567 (SEQ ID NO: 106) CLTA1-5-2 5 AGgCaTCATCTaCaTCAAGtTGG 0 41280 0 28896 0 35152 (SEQ ID NO: 107) CLTA1-5-3 5 AGTaaTCActTCCaTCAAGCCGG 0     0 0     0 0     0 (SEQ ID NO: 108) CLTA1-5-4 5 tccCCTCAcCTCCCTaAAGCAGG 2 24169 5 17512 1 23483 (SEQ ID NO: 109) CLTA1-5-5 5 tGTCtTtATtTCCCTCtAGCTGG 0 11527 0 10481 1 11027 (SEQ ID NO: 110) CLTA1-6-1 6 AGTCCTCATCTCCCTCAAGCAGG 0  6537 0  5654 0  6741 (SEQ ID NO: 111)

TABLE 4 no sgRNA v1.0 sgRNA v2.1 sgRNA modified total modified total modified m sequence sequences sequences sequences sequences sequences total sequences CLTA4-0-1 0 GCAGATGTAGTGTTTCCACAGGG 6 29191 2005    18640 14970     19661 (SEQ ID NO: 112) CLTA4-3-1 3 aCAtATGTAGTaTTTCCACAGGG 2 34165 11  20018 3874    16082 (SEQ ID NO: 113) CLTA4-3-2 3 GCAtATGTAGTGTTTCCAaATGt 3 17923 0 11688 2 13880 (SEQ ID NO: 114) CLTA4-3-3 3 cCAGATGTAGTaTTcCCACAGGG 0 16559 0 12007 52  11082 (SEQ ID NO: 115) CLTA4-3-4 3 GCAGtTtTAGTGTTTtCACAGGG 0 21722 0 12831 0 15726 (SEQ ID NO: 116) CLTA4-3-5 3 GCAGAgtTAGTGTTTCCACACaG 1 21222 2 13555 3 16425 (SEQ ID NO: 117) CLTA4-3-6 3 GCAGATGgAGgGTTTtCACAGGG 3 20342 3 12804 3 14068 (SEQ ID NO: 118) CLTA4-3-7 3 GgAaATtTAGTGTTTCCACAGGG 2 38894 3 24017 1 29347 (SEQ ID NO: 119) CLTA4-4-1 4 aaAGAaGTAGTaTTTCCACATGG 0     0 0     0 0     0 (SEQ ID NO: 120) CLTA4-4-2 4 aaAGATGTAGTcaTTCCACAAGG 1 27326 0 17365 1 18941 (SEQ ID NO: 121) CLTA4-4-3 4 aaAtATGTAGTcTTTCCACAGGG 2 46232 3 32264 0 32638 (SEQ ID NO: 122) CLTA4-4-4 4 atAGATGTAGTGTTTCCAaAGGa 9 27821 1 16223 8 15388 (SEQ ID NO: 123) CLTA4-4-5 4 cCAGAgGTAGTGcTcCCACAGGG 1 20979 1 15674 1 15086 (SEQ ID NO: 124) CLTA4-4-6 4 cCAGATGTgagGTTTCCACAAGG 4 22021 0 15691 1 14253 (SEQ ID NO: 125) CLTA4-4-7 4 ctAcATGTAGTGTTTCCAtATGG 2 35942 0 23076 1 11867 (SEQ ID NO: 126) CLTA4-4-8 4 ctAGATGaAGTGcTTCCACATGG 1 10692 1  7609 59   8077 (SEQ ID NO: 127) CLTA4-4-9 4 GaAaATGgAGTGTTTaCACATGG 0 34616 0 22302 1 24671 (SEQ ID NO: 128) CLTA4-4-10 4 GCAaATGaAGTGTcaCCACAAGG 1 25210 0 16187 0 16974 (SEQ ID NO: 129) CLTA4-4-11 4 GCAaATGTAtTaTTTCCACtAGG 0 34144 1 24770 0 22547 (SEQ ID NO: 130) CLTA4-4-12 4 GCAGATGTAGctTTTgtACATGG 0 14254 0  9616 0  9994 (SEQ ID NO: 131) CLTA4-4-13 4 GCAGcTtaAGTGTTTtCACATGG 8 39466 1  7609 5 16525 (SEQ ID NO: 132) CLTA4-4-14 4 ttAcATGTAGTGTTTaCACACGG 0     0 0 22302 0     0 (SEQ ID NO: 133) CLTA4-5-1 5 GaAGAgGaAGTGTTTgCcCAGGG 1 27616 1 16319 1 16140 (SEQ ID NO: 134) CLTA4-5-2 5 GaAGATGTgGaGTTgaCACATGG 1 22533 0 14292 0 15013 (SEQ ID NO: 135) CLTA4-5-3 5 GCAGAaGTAcTGTTgttACAAGG 1 44243 1 29391 1 29734 (SEQ ID NO: 136) CLTA4-5-4 5 GCAGATGTgGaaTTaCaACAGGG 0 27321 0 13640 0 14680 (SEQ ID NO: 137) CLTA4-5-5 5 GCAGtcaTAGTGTaTaCACATGG 1 26538 0 18449 1 20559 (SEQ ID NO: 138) CLTA4-5-6 5 taAGATGTAGTaTTTCCAaAAGt 1 15145 1  8905 0  7911 (SEQ ID NO: 139) CLTA4-6-1 6 GCAGcTGgcaTtTcTCCACACGG 0     2 0     0 0     0 (SEQ ID NO: 140) CLTA4-6-2 6 GgAGATcTgaTGgTTCtACAAGG 2 27797 0 19450 2 21709 (SEQ ID NO: 141) CLTA4-6-3 6 taAaATGcAGTGTaTCCAtATGG 4 27551 0 18424 0 18783 (SEQ ID NO: 142) CLTA4-7-1 7 GCcagaaTAGTtTTTCaACAAGG 0 20942 0 13137 1 13792 (SEQ ID NO: 143) CLTA4-7-2 8 ttgtATtTAGaGaTTgCACAAGG 0 28470 0 18104 0 20416 (SEQ ID NO: 144)

TABLE 5 Off-target site Human genome coordinates CLTA1-0-1 9(+): 36,211,732-36,211,754 12(+): 7,759,893-7,759,915 CLTA1-1-1 8(−): 15,546,437-15,546,459 CLTA1-2-1 3(−): 54,223,111-54,223,133 CLTA1-2-2 15(+): 89,388,670-89,388,692 CLTA1-2-3 5(+): 88716920-88,716,942 CLTA1-3-1 21(+): 27,972,462-27,972,484 CLTA1-3-2 4(−): 17,179,924-17,179,946 CLTA1-4-1 1(+): 147,288,742-147,288,764 CLTA1-4-2 10(+): 97,544,444-97,544,466 CLTA1-4-3 2(−): 161,873,870-161,873,892 CLTA1-4-4 1(+): 196,172,702-196,172,724 CLTA1-4-5 13(+): 56,574,636-56,574,658 CLTA1-4-6 2(+): 241,357,827-241,357,849 CLTA1-4-7 3(+): 121,248,627-121,248,649 CLTA1-4-8 12(+): 132,937,319-132,937,341 CLTA1-5-1 9(−): 80,930,919-80,930,941 CLTA1-5-2 2(+): 140,901,875-14,0901,897 CLTA1-5-3 3(+): 45,016,841-45,016,863 CLTA1-5-4 X(+): 40,775,684-40,775,706 CLTA1-5-5 2(−): 185,151,622-185,151,644 CLTA1-6-1 X(+): 150,655,097-150,655,119 CLTA4-0-1 9(−): 36,211,779-36,211,801 CLTA4-3-1 12(−): 50,679,419-50,679,441 CLTA4-3-2 X(−): 143,939,483-143,939,505 CLTA4-3-3 11(−): 47,492,611-47,492,633 CLTA4-3-4 3(−): 162,523,715-162,523,737 CLTA4-3-5 11(+): 30,592,975-30,592,997 CLTA4-3-6 4(−): 155,252,699-155,252,721 CLTA4-3-7 18(+): 39,209,441-39,209,463 CLTA4-4-1 17(−): 36,785,650-36,785,672 CLTA4-4-2 1(−): 241,537,119-241,537,141 CLTA4-4-3 8(−): 120,432,103-120,432,125 CLTA4-4-4 6(−): 106,204,600-106,204,622 CLTA4-4-5 8(+): 102,527,804-102,527,826 CLTA4-4-6 8(−): 94,685,538-94,685,560 CLTA4-4-7 2(+): 35,820,054-35,820,076 CLTA4-4-8 3(−): 36,590,352-36,590,374 CLTA4-4-9 12(+): 100,915,498-100,915,520 CLTA4-4-10 21(+): 33,557,705-33,557,727 CLTA4-4-11 8(+): 10,764,183-10,764,205 CLTA4-4-12 19(+): 37,811,645-37,811,667 CLTA4-4-13 13(−): 26,832,673-26,832,695 CLTA4-4-14 6(+): 19,349,572-19,349,594 CLTA4-5-1 11(−): 502,300-502,322 CLTA4-5-2 8(−): 28,389,683-28,389,705 CLTA4-5-3 2(−): 118,557,405-118,557,427 CLTA4-5-4 2(−): 103,248,360-103,248,382 CLTA4-5-5 21(−) : 42,929,085-42,929,107 CLTA4-5-6 13(−): 83,097,278-83,097,300 CLTA4-6-1 2(+): 43,078,423-43,078,445 CLTA4-6-2 7(−): 11,909,384-11,909,406 CLTA4-6-3 5(−): 69,775,482-69,775,504 CLTA4-7-1 16(+): 30,454,945-30,454,967 CLTA4-7-2 9(−): 77,211,328-77,211,350

TABLE 6 in vitro modification frequency number of enrichment in HEK293T cells mutations sequence gene v1.0 v2.1 no sgRNA v1.0 v2.1 CLTA1-0-1 0 AGTCCTCATCTCCCTCAAGCAGG CLTA 41.4 23.3 0.003% 0.042% 0.337% (SEQ ID NO: 145) CLTA1-1-1 1 AGTCCTCAaCTCCCTCAAGCAGG TUSC3 25.9 14   0.003% 0.031% 0.091% (SEQ ID NO: 146) CLTA1-2-1 2 AGcCCTCATtTCCCTCAAGCAGG CACNA2D3 15.4 26.2     0%     0%     0% (SEQ ID NO: 147) CLTA1-2-2 2 AcTCCTCATCcCCCTCAAGCCGG ACAN 29.2 18.8 0.014% 0.005% 0.146% (SEQ ID NO: 148) CLTA1-2-3 2 AGTCaTCATCTCCCTCAAGCAGa   0.06   1.27 n.t. n.t. n.t. (SEQ ID NO: 149) CLTA1-3-1 3 cGTCCTCcTCTCCCcCAAGCAGG 0    2.07 0.004%     0%     0% (SEQ ID NO: 150) CLTA1-3-2 3 tGTCCTCtTCTCCCTCAAGCAGa BC029598 0    1.47     0%     0%     0% (SEQ ID NO: 151) CLTA1-4-1 4 AagCtTCATCTCtCTCAAGCTGG     0% 0.006%     0% (SEQ ID NO: 152) CLTA1-4-2 4 AGTaCTCtTtTCCCTCAgGCTGG ENTPD1 0.007% 0.004% 0.015% (SEQ ID NO: 153) CLTA1-4-3 4 AGTCtTaAatTCCCTCAAGCAGG 0.003%     0% 0.001% (SEQ ID NO: 154) CLTA1-4-4 4 AGTgCTCATCTaCCagAAGCTGG 0.008%     0%     0% (SEQ ID NO: 155) CLTA1-4-5 4 ccTCCTCATCTCCCTgcAGCAGG 0.013% 0.004%     0% (SEQ ID NO: 156) CLTA1-4-6 4 ctaCaTCATCTCCCTCAAGCTGG     0% 0.008% 0.016% (SEQ ID NO: 157) CLTA1-4-7 4 gGTCCTCATCTCCCTaAAaCAGa POLQ (coding) 0.011% 0.037% 0% (SEQ ID NO: 158) CLTA1-4-8 4 tGTCCTCATCggCCTCAgGCAGG     0%     0% 0.016% (SEQ ID NO: 159) CLTA1-5-1 5 AGaCacCATCTCCCTtgAGCTGG PSAT1     0% 0.003% 0.006% (SEQ ID NO: 160) CLTA1-5-2 5 AGgCaTCATCTaCaTCAAGtTGG     0%     0%     0% (SEQ ID NO: 161) CLTA1-5-3 5 AGTaaTCActTCCaTCAAGCCGG ZDHHC3, n.t. n.t. n.t. (SEQ ID NO: 162) EXOSC7 CLTA1-5-4 5 tccCCTCAcCTCCCTaAAGCAGG 0.008% 0.029% 0.004% (SEQ ID NO: 163) CLTA1-5-5 5 tGTCtTtATtTCCCTCtAGCTGG     0%     0% 0.009% (SEQ ID NO: 164) CLTA1-6-1 6 AGTCCTCATCTCCCTCAAGCAGG     0%     0%     0% (SEQ ID NO: 165)

TABLE 7 # of sequences sequence no sgRNA v1.0 sgRNA v2.1 sgRNA CLTA1-0-1 ref AGTCCTCATCTCCCTCAAGCAGG (SEQ ID 58,887 42,665 52,667 NO: 166) AGTCCTCATCTCCCTCA A AGCAGG (SEQ ID 0 0 66 NO: 167) AGTCCTCATCTCCCTC-AGCAGG (SEQ ID 0 2 28 NO: 168) AGTCCTCAT-------------- 0 0 13 AGTCCTCATCTCCCTCA T AGCAGG (SEQ ID 0 0 11 NO: 169) AGTCCTCAT--------AGCAGG (SEQ ID 0 0 9 NO: 170) AGTCCTCATCT------AGCAGG (SEQ ID 0 0 8 NO: 171) AGTCCTCA---------AGCAGG (SEQ ID 0 0 6 NO: 172) AGTCCTCATCTCCCTCA AAGGCAGTGTTTGTT 0 0 4 ACTTGAGTTTGTC AGCAGG (SEQ ID NO: 173) AGTCCTCATCTCCCTCA TT AGCAGG (SEQ ID 0 0 4 NO: 174) AGTCCTCATCTCCCTCA GGGCTTGTTTACAGC 0 0 3 TCACCTTTGAATTTGCACAAGCGTGCA AGCAG G (SEQ ID NO: 175) AGTCCTCATCTCCCT-AGCAGG (SEQ ID 0 11 0 NO: 176) AGTCCTCATCCCTC-AAGCAGG (SEQ ID 0 3 0 NO: 177) AGTCCTCATCTCCCT-AAGCAGG (SEQ ID 1 2 0 NO: 178) other 1 0 26 modified total 2 18 178 (0.042%) (0.34%) CLTA1-1-1 ref AGTCCTCATCTCCCTCAAGCAGG (SEQ ID 39,803 28,991 40,551 NO: 179) AGTCCTCAaCTCCCTCA A AGCAGG (SEQ ID 0 4 13 NO: 180) AGTCCTCAaCTCCCTCA------ (SEQ ID 0 0 12 NO: 181) AGTCCTCAaCTCCCTC-AGCAGG (SEQ ID 0 2 4 NO: 182) AGTCCTCAaCTCCCTCA AGAAAGGTGTTGAAAA 0 0 3 TCAGAAAGAGAGAAACA AGCAGG (SEQ ID NO: 183) AGTCCTCAaCTCCCTCA ATCTACGGTCCATTCC 0 0 2 CGTTTCCACTCACCTTGCGCCGC AGCAGG (SEQ ID NO: 184) AGTCCTCAaCTCCCT-AAGCAGG (SEQ ID 0 3 1 NO: 185) AGTCCTCAaCTCCCTCA ACCAACTTTAACATCC 0 0 1 T GCTGGTTCTGTCATTAATAAGTTGAA AGCAGG (SEQ ID NO: 186) AGTCCTCAaCTCCCTCA CAGCAAATAAAAAAGT 0 0 1 TGTTTATGCATATTCAGATAAGCAA AGCAGG (SEQ ID NO: 187) AGTCCTCAaCTCCC-AAGCAGG (SEQ ID 1 0 0 NO: 188) modified total 1 9 37 (0.031%) (0.091%) CLTA1-2-2 ref AcTCCTCATCcCCCTCAAGCCGG (SEQ ID 21,264 20,041 22,546 NO: 189) AcTCCTCATCcCCCTCA A AGCCGG (SEQ ID 0 0 8 NO: 190) AcTCCTCATCcCCCTCA G AGCCGG (SEQ ID 0 0 7 NO: 191) AcTCCTC-----------AGCCGG (SEQ ID 0 0 5 NO: 192) AcTCCTCATCcCCCTCA AA AGCCGG (SEQ ID 0 0 2 NO: 193) AcTCCTCATCcCCCTCA GC AGCCGG (SEQ ID 0 0 2 NO: 194) AcTCCTCATCcCCCTCA T AGCCGG (SEQ ID 0 0 2 NO: 195) AcTCCTCATCcCCCTCA TCC CCGG (SEQ ID 0 0 2 NO: 196) AcTCCTCATCcC-----AGCCGG (SEQ ID 0 0 2 NO: 197) AcTCCTCATCcCCCTA-AGCCGG (SEQ ID 3 1 1 NO: 198) AcTCCTCATCcCCCTCA AT AGCCGG (SEQ ID 0 0 1 NO: 199) AcTCCTCACCcCCCTCA GC AGCCGG (SEQ ID 0 0 1 NO: 200) modified total 3 1 33 (0.15%)

TABLE 8 # of sequences sequence control v1.0 sgRNA v2.1 sgRNA CLTA4-0-1 ref GCAGATGTAGTGTTTCCACAGGG 29,185 16,635 17,555 (SEQ ID NO: 201) GCAGATGTAGTGTTTC-ACAGGG 1 891 5,937 (SEQ ID NO: 202) GCAGATGTAGTGTTTCC C ACAGGG 0 809 5,044 (SEQ ID NO: 203) GCAGATGTAGTG----CACAGGG 0 14 400 (SEQ ID NO: 204) GCAGATGTAGTGTTTCC-CAGGG 0 19 269 (SEQ ID NO: 205) GCAGATGTAC-------ACAGGG 0 17 262 (SEQ ID NO: 206) GCAGATGTAGTGTCA---CAGGG 2 6 254 (SEQ ID NO: 207) GCAGATGTAGTGTTCA-CAGGG (SEQ 0 21 229 ID NO: 208) GCAGATGTAGTGTTTC-CAGGG (SEQ 1 14 188 ID NO: 209) GCAGATGTAGT-----CACAGGG 0 0 152 (SEQ ID NO: 210) GCAGATGT-----------AGGG 0 6 129 (SEQ ID NO: 211) other 2 208 2,106 modified total 6 2,005 14,970 (11%) (76%) CLTA4-3-1 ref aCAtATGTAGTaTTTCCACAGGG 34,163 20,007 12,208 (SEQ ID NO: 212) aCAtATGTAGTaTTTCC C ACAGGG 0 8 1779 (SEQ ID NO: 213) aCAtATGTAGTaTTTCA-CAGGG 1 0 293 (SEQ ID NO: 214) aCAtATGTAGTaTTTC-CAGGG (SEQ 1 0 227 ID NO: 215) aCAtAT----------CACAGGG 0 0 117 (SEQ ID NO: 216) a-----------------CAGGG 0 0 96 aCAt------------CACAGGG 0 0 78 (SEQ ID NO: 217) aCAtATGTAGT-----CACAGGG 0 0 77 (SEQ ID NO: 218) aCAtATGTAGTaTTTCC------ 0 0 76 (SEQ ID NO: 219) aCAtATGT-----------AGGG 0 0 68 (SEQ ID NO: 220) aCAtATGTAG------CACAGGG 0 0 64 (SEQ ID NO: 221) other 0 3 999 modified total 2 11 3874 (0.055%) (24%) CLTA4-3-3 ref cCAGATGTAGTaTTcCCACAGGG 16,559 12,007 11,030 (SEQ ID NO: 222) cCAGATGTAGTaTTcCC C ACAGGG 0 0 35 (SEQ ID NO: 223) cCAGATGTAGTaT----ACAGGG 0 0 5 (SEQ ID NO: 224) cCAGATGTAGTaT---CACAGGG 0 0 3 (SEQ ID NO: 225) cCAGATGTAGTaTTcCC AAC ACAGGG 0 0 2 (SEQ ID NO: 226) cCAGATGTAGTaTT-CACAGGG (SEQ 0 0 2 ID NO: 227) cCAGATGTAGTaTTcC-CAGGG (SEQ 0 0 2 ID NO: 228) cCAGATGTA-------------- 0 0 2 cCAGATGTAGTaTTcC-ACAGGG 0 0 1 (SEQ ID NO: 229) modified total 0 0 52 (0.47%) CLTA4-4-8 ref ctAGATGaAGTGcTTCCACATGG 10,691 7,608 8,018 (SEQ ID NO: 230) ctAGATGaAGTGcTTCC C ACATGG 0 0 49 (SEQ ID NO: 231) ctAGATGaAGTGcTTC-ACATGG 0 0 6 (SEQ ID NO: 232) ctAGATGaAGTG----------- 0 0 2 (SEQ ID NO: 233) ctAGATGaAGTGcTTCC A CACATGG 0 0 1 (SEQ ID NO: 234) ctAGATGaAGTGcTTC-CATGG (SEQ 1 0 0 ID NO: 235) ctAGATGaAGTGcTTCC-CATGG 0 1 0 (SEQ ID NO: 236) modified total 1 1 59 (0.73%)

TABLE 9 oligonucleotide name oligonucleotide sequence (5′->3′) CLTA1 v2.1 template fwd TAA TAC GAC TCA CTA TAG GAG TCC TCA TCT CCC TCA AGC GTT TTA GAG CTA TGC TG (SEQ ID NO: 237) CLTA2 v2.1 template fwd TAA TAC GAC TCA CTA TAG GCT CCC TCA AGC AGG CCC CGC GTT TTA GAG CTA TGC TG (SEQ ID NO: 238) CLTA3 v2.1 template fwd TAA TAC GAC TCA CTA TAG GTG TGA AGA GCT TCA CTG AGT GTT TTA GAG CTA TGC TG (SEQ ID NO: 239) CLTA4 v2.1 template fwd TAA TAC GAC TCA CTA TAG GGC AGA TGT AGT GTT TCC ACA GTT TTA GAG CTA TGC TG (SEQ ID NO: 240) v2.1 template rev GAT AAC GGA CTA GCC TTA TTT TAA CTT GCT ATG CTT TTC AGC ATA GCT CTA AAA C (SEQ ID NO: 241) CLTA1 v1.0 template CGG ACT AGC CTT ATT TTA ACT TGC TAT TTC TAG CTC TAA AAC GCT TGA GGG AGA TGA GGA CTC CTA TAG TGA GTC GTA TTA (SEQ ID NO: 242) CLTA2 v1.0 template CGG ACT AGC CTT ATT TTA ACT TGC TAT TTC TAG CTC TAA AAC GCG GGG CCT GCT TGA GGG AGC CTA TAG TGA GTC GTA TTA (SEQ ID NO: 243) CLTA3 v1.0 template CGG ACT AGC CTT ATT TTA ACT TGC TAT TTC TAG CTC TAA AAC ACT CAG TGA AGC TCT TCA CAC CTA TAG TGA GTC GTA TTA (SEQ ID NO: 244) CLTA4 v1.0 template CGG ACT AGC CTT ATT TTA ACT TGC TAT TTC TAG CTC TAA AAC TGT GGA AAC ACT ACA TCT GCC CTA TAG TGA GTC GTA TTA (SEQ ID NO: 245) T7 promoter oligo TAA TAC GAC TCA CTA TAG G (SEQ ID NO: 246) CLTA1 lib /5Phos/AAC ACA NNN NC*C* NG*C* T*T*G* A*G*G* G*A*G* A*T*G* A*G*G* A*C*T* NNN NAC CTG CCG AGA ACA CA (SEQ ID NO: 247) CLTA2 lib /5Phos/TCT TCT NNN NC*C* NG*C* G*G*G* G*C*C* T*G*C* T*T*G* A*G*G* G*A*G* NNN NAC CTG CCG AGT CTT CT (SEQ ID NO: 248) CLTA3 lib /5Phos/AGA GAA NNN NC*C* NA*C* T*C*A* G*T*G* A*A*G* C*T*C* T*T*C* A*C*A* NNN NAC CTG CCG AGA GAG AA (SEQ ID NO: 249) CLTA4 lib /5Phos/TTG TGT NNN NC*C* NT*G* T*G*G* A*A*A* C*A*C* T*A*C* A*T*C* T*G*C* NNN NAC CTG CCG AGT TGT GT (SEQ ID NO: 250) CLTA1 site fwd CTA GCA GTC CTC ATC TCC CTC AAG CAG GC (SEQ ID NO: 251) CLTA1 site rev AGC TGC CTG CTT GAG GGA GAT GAG GAC TG (SEQ ID NO: 252) CLTA2 site fwd CTA GTC TCC CTC AAG CAG GCC CCG CTG GT (SEQ ID NO: 253) CLTA2 site rev AGC TAC CAG CGG GGC CTG CTT GAG GGA GA (SEQ ID NO: 254) CLTA3 site fwd CTA GCT GTG AAG AGC TTC ACT GAG TAG GA (SEQ ID NO: 255) CLTA3 site rev AGC TTC CTA CTC AGT GAA GCT CTT CAC AG (SEQ ID NO: 256) CLTA4 site fwd CTA GTG CAG ATG TAG TGT TTC CAC AGG GT (SEQ ID NO: 257) CLTA4 site rev AGC TAC CCT GTG GAA ACA CTA CAT CTG CA (SEQ ID NO: 258) test fwd GCG ACA CGG AAA TGT TGA ATA CTC AT (SEQ ID NO: 259) test rev GGA GTC AGG CAA CTA TGG ATG AAC G (SEQ ID NO: 260) off-target CLTA4-0 fwd ACT GTG AAG AGC TTC ACT GAG TAG GAT TAA GAT ATT GCA GAT GTA GTG TTT CCA CAG GGT (SEQ ID NO: 261) off-target CLTA4-1 fwd ACT GTG AAG AGC TTC ACT GAG TAG GAT TAA GAT ATT GAA GAT GTA GTG TTT CCA CAG GGT (SEQ ID NO: 262) off-target CLTA4-2a fwd ACT GTG AAG AGC TTC ACT GAG TAG GAT TAA GAT ATT GAA GAT GTA GTG TTT CCA CTG GGT (SEQ ID NO: 263) off-target CLTA4-2b fwd ACT GTG AAG AGC TTC ACT GAG TAG GAT TAA GAT ATT GCA GAT GGA GGG TTT CCA CAG GGT (SEQ ID NO: 264) off-target CLTA4-2c fwd ACT GTG AAG AGC TTC ACT GAG TAG GAT TAA GAT ATT GCA GAT GTA GTG TTA CCA GAG GGT (SEQ ID NO: 265) off-target CLTA4-3 fwd ACT GTG AAG AGC TTC ACT GAG TAG GAT TAA GAT ATT GGG GAT GTA GTG TTT CCA CTG GGT (SEQ ID NO: 266) off-target CLTA4-0 rev TCC CTC AAG CAG GCC CCG CTG GTG CAC TGA AGA GCC ACC CTG TGG AAA CAC TAC ATC TGC (SEQ ID NO: 267) off-target CLTA4-1 rev TCC CTC AAG CAG GCC CCG CTG GTG CAC TGA AGA GCC ACC CTG TGG AAA CAC TAC ATC TTC (SEQ ID NO: 268) off-target CLTA4-2a rev TCC CTC AAG CAG GCC CCG CTG GTG CAC TGA AGA GCC ACC CAG TGG AAA CAC TAC ATC TTC (SEQ ID NO: 269) off-target CLTA4-2b rev TCC CTC AAG CAG GCC CCG CTG GTG CAC TGA AGA GCC ACC CTG TGG AAA CCC TCC ATC TGC (SEQ ID NO: 270) off-target CLTA4-2c rev TCC CTC AAG CAG GCC CCG CTG GTG CAC TGA AGA GCC ACC CTC TGG TAA CAC TAC ATC TGC (SEQ ID NO: 271) off-target CLTA4-3 rev TCC CTC AAG CAG GCC CCG CTG GTG CAC TGA AGA GCC ACC CAG TGG AAA CAC TAC ATC CCC (SEQ ID NO: 272) adapter1(AACA) AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TAA CA (SEQ ID NO: 273) adapter2(AACA) TGT TAG ATC GGA AGA GCG TCG TGT AGG GAA AGA GTG TAG ATC TCG GTG G (SEQ ID NO: 274) adapter1(TTCA) AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TTT CA (SEQ ID NO: 275) adapter2(TTCA) TGA AAG ATC GGA AGA GCG TCG TGT AGG GAA AGA GTG TAG ATC TCG GTG G (SEQ ID NO: 276) adapter1 AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC T (SEQ ID NO: 277) adapter2 AGA TCG GAA GAG CGT CGT GTA GGG AAA GAG TGT AGA TCT CGG TGG (SEQ ID NO: 278) lib adapter1 GAC GGC ATA CGA GAT (SEQ ID NO: 279) CLTA1 lib adapter2 AAC AAT CTC GTA TGC CGT CTT CTG CTT G (SEQ ID NO: 280) CLTA2 lib adapter2 TCT TAT CTC GTA TGC CGT CTT CTG CTT G (SEQ ID NO: 281) CLTA3 lib adapter2 AGA GAT CTC GTA TGC CGT CTT CTG CTT G (SEQ ID NO: 282) CLTA4 lib adapter2 TTG TAT CTC GTA TGC CGT CTT CTG CTT G (SEQ ID NO: 283) CLTA1 sel PCR CAA GCA GAA GAC GGC ATA CGA GAT TGT GTT CTC GGC AGG T (SEQ ID NO: 284) CLTA2 sel PCR CAA GCA GAA GAC GGC ATA CGA GAT AGA AGA CTC GGC AGG T (SEQ ID NO: 285) CLTA3 sel PCR CAA GCA GAA GAC GGC ATA CGA GAT TTC TCT CTC GGC AGG T (SEQ ID NO: 286) CLTA4 sel PCR CAA GCA GAA GAC GGC ATA CGA GAT ACA CAA CTC GGC AGG T (SEQ ID NO: 287) PE2 short AAT GAT ACG GCG ACC ACC GA (SEQ ID NO: 288) CLTA1 lib seq PCR AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TNN NNA CCT ACC TGC CGA GAA CAC A (SEQ ID NO: 289) CLTA2 lib seq PCR AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TNN NNA CCT ACC TGC CGA GTC TTC T (SEQ ID NO: 290) CLTA3 lib seq PCR AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TNN NNA CCT ACC TGC CGA GAG AGA A (SEQ ID NO: 291) CLTA4 lib seq PCR AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TNN NNA CCT ACC TGC CGA GTT GTG T (SEQ ID NO: 292) lib fwd PCR CAA GCA GAA GAC GGC ATA CGA GAT (SEQ ID NO: 293) CLTA1-0-1 (Chr. 9) fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT CAA GTC TAG CAA GCA GGC CA (SEQ ID NO: 294) CLTA1-0-1 (Chr. 12) fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT CAG GCA CTG AGT GGG AAA GT (SEQ ID NO: 295) CLTA1-1-1 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TAA CCC CAA GTC AGC AAG CA (SEQ ID NO: 296) CLTA1-2-1 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TTG CTG GTC AAT ACC CTG GC (SEQ ID NO: 297) CLTA1-2-2 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TGA GTA CCC CTG AAA TGG GC (SEQ ID NO: 298) CLTA1-3-1 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TCG CTA CCA ATC AGG GCT TT (SEQ ID NO: 299) CLTA1-3-2 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT CCA TTG CCA CTT GTT TGC AT (SEQ ID NO: 300) CLTA1-4-1 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT CCT ACC CCC ACA ACT TTG CT (SEQ ID NO: 301) CLTA1-4-2 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT GTG TAC ATC CAG TGC ACC CA (SEQ ID NO: 302) CLTA1-4-3 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TCG GAA AGG ACT TTG AAT ACT TGT (SEQ ID NO: 303) CLTA1-4-4 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT CGG CCC AAG ACC TCA TTC AC (SEQ ID NO: 304) CLTA1-4-5 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT GTC CTC TCT GGG GCA GAA GT (SEQ ID NO: 305) CLTA1-4-6 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT AGC TGA GTC ATG AGT TGT CTC C (SEQ ID NO: 306) CLTA1-4-7 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT CTG CCA GCT TCT CAC ACC AT (SEQ ID NO: 307) CLTA1-4-8 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT CTG AAG GAC AAA GGC GGG AA (SEQ ID NO: 308) CLTA1-5-1 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT AAG GTG CTA AAG GCT CCA CG (SEQ ID NO: 309) CLTA1-5-2 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT GAC CAT TGG TGA GCC CAG AG (SEQ ID NO: 310) CLTA1-5-3 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TTT TTC GGG CAA CTG CTC AC (SEQ ID NO: 311) CLTA1-5-4 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT GCA AGC CTT CTC TCC TCA GA (SEQ ID NO: 312) CLTA1-5-5 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT ACA CAA ACT TCC CTG AGA CCC (SEQ ID NO: 313) CLTA1-6-1 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TGA GTT AGC CCT GCT GTT CA (SEQ ID NO: 314) CLTA4-0-1 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TGA AGA GCT TCA CTG AGT AGG A (SEQ ID NO: 315) CLTA4-3-1 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TCC CCT TAC AGC CAA TTT CGT (SEQ ID NO: 316) CLTA4-3-2 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TGC TGA TGA AAT GCA ATT AAG AGG T (SEQ ID NO: 317) CLTA4-3-3 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT GGT CCC TGC AAG CCA GTA TG (SEQ ID NO: 318) CLTA4-3-4 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT ATC AAA GCC TTG TAT CAC AGT T (SEQ ID NO: 319) CLTA4-3-5 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT CCC AAA TAA TGC AGG AGC CAA (SEQ ID NO: 320) CLTA4-3-6 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT CTG CCT TTA GTG GGA CAG ACT T (SEQ ID NO: 321) CLTA4-3-7 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT AGT AAC CCT AGT AGC CCT CCA (SEQ ID NO: 322) CLTA4-4-1 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT CAT TGC AGT GAG CCG AGA TTG (SEQ ID NO: 323) CLTA4-4-2 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TGG CAA AGT TCA CTT CCA TGT (SEQ ID NO: 324) CLTA4-4-3 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TGC TCT GTG ATG TCT GCC AC (SEQ ID NO: 325) CLTA4-4-4 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TGT GTA GGA TTG TGA ACC AGC A (SEQ ID NO: 326) CLTA4-4-5 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TCC CAG CCC AGC ATT TTT CT (SEQ ID NO: 327) CLTA4-4-6 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT AGG TTG CTT TGT GCA CAG TC (SEQ ID NO: 328) CLTA4-4-7 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT CCT GGC TTG GGA TGT TGG AA (SEQ ID NO: 329) CLTA4-4-8 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TTG CCC AAG GTC ATA CTG CT (SEQ ID NO: 330) CLTA4-4-9 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT ACC CAC TAG GTA GCC ATA ATC CA (SEQ ID NO: 331) CLTA4-4-10 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT CGG TCA TGT CGC TTG GAA GA (SEQ ID NO: 332) CLTA4-4-11 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TTG GCC CAT ATT GCT TTA TGC TG (SEQ ID NO: 333) CLTA4-4-12 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT ATT AGG GGT TGG CTG CAT GA (SEQ ID NO: 334) CLTA4-4-13 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT CCA AGA CGT GTT GCA TGC TG (SEQ ID NO: 335) CLTA4-4-14 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TGG GAG GTG ATA AAT TCC CTA AAT (SEQ ID NO: 336) CLTA4-5-1 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT CCA GAG ACA AAG GTG GGG AG (SEQ ID NO: 337) CLTA4-5-2 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TCA TAC AGA AGA GCA AAG TAC CA (SEQ ID NO: 338) CLTA4-5-3 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT CAA AGA GGG GTA TCG GGA GC (SEQ ID NO: 339) CLTA4-5-4 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT AAA TGG AAG AAC CAA GTA GAT GAA (SEQ ID NO: 340) CLTA4-5-5 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TTT TGG TTG ACA GAT GGC CAC A (SEQ ID NO: 341) CLTA4-5-6 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TCT TAC TTG TGT GAT TTT AGA ACA A (SEQ ID NO: 342) CLTA4-6-1 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT GAT GGT TCA TGC AGA GGG CT (SEQ ID NO: 343) CLTA4-6-2 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT GCT GGT CTT TCC TGA GCT GT (SEQ ID NO: 344) CLTA4-6-3 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT CTC CAT CAG ATA CCT GTA CCC A (SEQ ID NO: 345) CLTA4-7-1 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT GGG AAA ACA CTC TCT CTC TGC T (SEQ ID NO: 346) CLTA4-7-2 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT GGA GGC CAC GAC ACA CAA TA (SEQ ID NO: 347) CLTA1-0-1 (Chr. 9) rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT CAC AGG GTG GCT CTT CAG TG (SEQ ID NO: 348) CLTA1-0-1 (Chr. 12) rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT TGC ACA TGT TTC CAC AGG GT (SEQ ID NO: 349) CLTA1-1-1 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT AGT GTT TCC AGG AGC GGT TT (SEQ ID NO: 350) CLTA1-2-1 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT AAG CCT CAG GCA CAA CTC TG (SEQ ID NO: 351) CLTA1-2-2 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT TAG GGG AGG GGC AAA GAC A (SEQ ID NO: 352) CLTA1-3-1 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT GGG AAC AGT GGT ATG CTG GT (SEQ ID NO: 353) CLTA1-3-2 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT AGT GTG GAC ACT GAC AAG GAA (SEQ ID NO: 354) CLTA1-4-1 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT TCA CTG CCT GGG TGC TTT AG (SEQ ID NO: 355) CLTA1-4-2 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT TAC CCC AGC CTC CAG CTT TA (SEQ ID NO: 356) CLTA1-4-3 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT TGA CTA CTG GGG AGC GAT GA (SEQ ID NO: 357) CLTA1-4-4 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT AGG CTG TTA TGC AGG AAA GGA A (SEQ ID NO: 358) CLTA1-4-5 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT GCG GTT GAG GTG GAT GGA AG (SEQ ID NO: 359) CLTA1-4-6 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT GGC AGC ATC CCT TAC ATC CT (SEQ ID NO: 360) CLTA1-4-7 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT AGA AAA AGC TTC CCC AGA AAG GA (SEQ ID NO: 361) CLTA1-4-8 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT CTG CAC CAA CCT CTA CGT CC (SEQ ID NO: 362) CLTA1-5-1 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT CTG GAG AGG GCA TAG TTG GC (SEQ ID NO: 363) CLTA1-5-2 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT TGG AAG GCT CTT TGT GGG TT (SEQ ID NO: 364) CLTA1-5-3 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT TTC CTA GCG GGA ACT GGA AA (SEQ ID NO: 365) CLTA1-5-4 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT AGG CTA ATG GGG TAG GGG AT (SEQ ID NO: 366) CLTA1-5-5 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT TGT CCA TGT TGG CTG AGG TG (SEQ ID NO: 367) CLTA1-6-1 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT CAG GCC AAC CTT GAC AAC TT (SEQ ID NO: 368) CLTA4-0-1 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT AGC AGG CCA AAG ATG TCT CC (SEQ ID NO: 369) CLTA4-3-1 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT TCT GCT CTT GAG GTT ATT TGT CC (SEQ ID NO: 370) CLTA4-3-2 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT GGG ACC AAT TTG CTA CTC ATG G (SEQ ID NO: 371) CLTA4-3-3 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT TGG AGG CTG TAA ACG TCC TG (SEQ ID NO: 372) CLTA4-3-4 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT TGC TAT GAT TTG CTG AAT TAC TCC T (SEQ ID NO: 373) CLTA4-3-5 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT GCA ATT TTG CAG ACC ACC ATC (SEQ ID NO: 374) CLTA4-3-6 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT GGC AGC TTG CAA CCT TCT TG (SEQ ID NO: 375) CLTA4-3-7 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT TCA TGA GAG TTT CCC CAA CA (SEQ ID NO: 376) CLTA4-4-1 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT ACT TGA GGG GGA AAA AGT TTC TTA (SEQ ID NO: 377) CLTA4-4-2 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT TGG TCC CTG TCT GTC ATT GG (SEQ ID NO: 378) CLTA4-4-3 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT AAG CGA GTG ACT GTC TGG GA (SEQ ID NO: 379) CLTA4-4-4 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT CAT GGG TGG GAC ACG TAG TT (SEQ ID NO: 380) CLTA4-4-5 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT GGC TTT CCT GGA CAC CCT ATC (SEQ ID NO: 381) CLTA4-4-6 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT AGA GCG AGG GAG CGA TGT A (SEQ ID NO: 382) CLTA4-4-7 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT TTG TGG ACC ACT GCT TAG TGC (SEQ ID NO: 383) CLTA4-4-8 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT CAA CTA CCC TGA GGC CAC C (SEQ ID NO: 384) CLTA4-4-9 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT GGT CAG CAC TCC TCA GCT TT (SEQ ID NO: 385) CLTA4-4-10 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT TGG AGG ATG CAT GCC ACA TT (SEQ ID NO: 386) CLTA4-4-11 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT CCC AGC CTC TTT GAC CCT TC (SEQ ID NO: 387) CLTA4-4-12 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT CCC ACA CCA GGC TGT AAG G (SEQ ID NO: 388) CLTA4-4-13 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT TAG ATA TAT GGG TGT GTC TGT ACG (SEQ ID NO: 389) CLTA4-4-14 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT TTC CAA AGT GGC TGA ACC AT (SEQ ID NO: 390) CLTA4-5-1 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT CCC ACA GGG CTG ATG TTT CA (SEQ ID NO: 391) CLTA4-5-2 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT TTG TAA TGC AAC CTC TGT CAT GC (SEQ ID NO: 392) CLTA4-5-3 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT CCA GCT CCA GCA ATC CAT GA (SEQ ID NO: 393) CLTA4-5-4 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT TTT GGG AAA GAT AGC CCT GGA (SEQ ID NO: 394) CLTA4-5-5 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT CAA TGA AAC AGC GGG GAG GT (SEQ ID NO: 395) CLTA4-5-6 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT ACA ATC ACG TGT CCT TCA CT (SEQ ID NO: 396) CLTA4-6-1 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT CAG ATC CCT CCT GGG CAA TG (SEQ ID NO: 397) CLTA4-6-2 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT GTC AGG AGG CAA GGA GGA AC (SEQ ID NO: 398) CLTA4-6-3 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT ACT TCC TTC CTT TTG AGA CCA AGT (SEQ ID NO: 399) CLTA4-7-1 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT GCG GCA GAT TCC TGG TGA TT (SEQ ID NO: 400) CLTA4-7-2 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT GGT CAC CAT CAG CAC AGT CA (SEQ ID NO: 401) PE1-barcode1 CAA GCA GAA GAC GGC ATA CGA GAT ATA TCA GTG TGA CTG GAG TTC AGA CGT GTG CT (SEQ ID NO: 402) PE1-barcode2 CAA GCA GAA GAC GGC ATA CGA GAT TTT CAC CGG TGA CTG GAG TTC AGA CGT GTG CT (SEQ ID NO: 403) PE1-barcode3 CAA GCA GAA GAC GGC ATA CGA GAT CCA CTC ATG TGA CTG GAG TTC AGA CGT GTG CT (SEQ ID NO: 404) PE1-barcode4 CAA GCA GAA GAC GGC ATA CGA GAT TAC GTA CGG TGA CTG GAG TTC AGA CGT GTG CT (SEQ ID NO: 405) PE1-barcode5 CAA GCA GAA GAC GGC ATA CGA GAT CGA AAC TCG TGA CTG GAG TTC AGA CGT GTG CT (SEQ ID NO: 406) PE1-barcode6 CAA GCA GAA GAC GGC ATA CGA GAT ATC AGT ATG TGA CTG GAG TTC AGA CGT GTG CT (SEQ ID NO: 407) PE2-barcode1 AAT GAT ACG GCG ACC ACC GAG ATC TAC ACA TTA CTC GAC ACT CTT TCC CTA CAC GAC (SEQ ID NO: 408) PE2-barcode2 AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CCG GAG AAC ACT CTT TCC CTA CAC GAC (SEQ ID NO: 409) PE2-barcode3 AAT GAT ACG GCG ACC ACC GAG ATC TAC ACC GCT CAT TAC ACT CTT TCC CTA CAC GAC (SEQ ID NO: 410)

REFERENCES

-   1. Hockemeyer, D. et al. Genetic engineering of human pluripotent     cells using TALE nucleases. Nature biotechnology 29, 731-734 (2011). -   2. Zou, J. et al. Gene targeting of a disease-related gene in human     induced pluripotent stem and embryonic stem cells. Cell stem cell 5,     97-110 (2009). -   3. Hockemeyer, D. et al. Efficient targeting of expressed and silent     genes in human ESCs and iPSCs using zinc-finger nucleases. Nature     biotechnology 27, 851-857 (2009). -   4. Doyon, Y. et al. Heritable targeted gene disruption in zebrafish     using designed zinc-finger nucleases. Nature biotechnology 26,     702-708 (2008). -   5. Meng, X., Noyes, M. B., Zhu, L. J., Lawson, N. D. & Wolfe, S. A.     Targeted gene inactivation in zebrafish using engineered zinc-finger     nucleases. Nature biotechnology 26, 695-701 (2008). -   6. Sander, J. D. et al. Targeted gene disruption in somatic     zebrafish cells using engineered TALENs. Nature biotechnology 29,     697-698 (2011). -   7. Tesson, L. et al. Knockout rats generated by embryo     microinjection of TALENs. Nature biotechnology 29, 695-696 (2011). -   8. Cui, X. et al. Targeted integration in rat and mouse embryos with     zinc-finger nucleases. Nature biotechnology 29, 64-67 (2011). -   9. Perez, E. E. et al. Establishment of HIV-1 resistance in CD4+ T     cells by genome editing using zinc-finger nucleases. Nature     biotechnology 26, 808-816 (2008). -   10. NCT00842634, NCT01044654, NCT01252641, NCT01082926. -   11. Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease     in adaptive bacterial immunity. Science 337, 816-821 (2012). -   12. Cong, L. et al. Multiplex genome engineering using CRISPR/Cas     systems. Science 339, 819-823 (2013). -   13. Mali, P. et al. RNA-guided human genome engineering via Cas9.     Science 339, 823-826 (2013). -   14. Hwang, W. Y. et al. Efficient genome editing in zebrafish using     a CRISPR-Cas system. Nature biotechnology 31, 227-229 (2013). -   15. Jinek, M. et al. RNA-programmed genome editing in human cells.     eLife 2, e00471 (2013). -   16. Dicarlo, J. E. et al. Genome engineering in Saccharomyces     cerevisiae using CRISPR-Cas systems. Nucleic acids research (2013). -   17. Jiang, W., Bikard, D., Cox, D., Zhang, F. & Marraffini, L. A.     RNA-guided editing of bacterial genomes using CRISPR-Cas systems.     Nature biotechnology 31, 233-239 (2013). -   18. Sapranauskas, R. et al. The Streptococcus thermophilus     CRISPR/Cas system provides immunity in Escherichia coli. Nucleic     acids research 39, 9275-9282 (2011). -   19. Semenova, E. et al. Interference by clustered regularly     interspaced short palindromic repeat (CRISPR) RNA is governed by a     seed sequence. Proceedings of the National Academy of Sciences of     the United States of America 108, 10098-10103 (2011). -   20. Qi, L. S. et al. Repurposing CRISPR as an RNA-Guided Platform     for Sequence-Specific Control of Gene Expression. Cell 152,     1173-1183 (2013). -   21. Pattanayak, V., Ramirez, C. L., Joung, J. K. & Liu, D. R.     Revealing off-target cleavage specificities of zinc-finger nucleases     by in vitro selection. Nature methods 8, 765-770 (2011). -   22. Doyon, J. B., Pattanayak, V., Meyer, C. B. & Liu, D. R. Directed     evolution and substrate specificity profile of homing endonuclease     I-SceI. Journal of the American Chemical Society 128, 2477-2484     (2006). -   23. Jiang, W., Bikard, D., Cox, D., Zhang, F. & Marraffini, L. A.     RNA-guided editing of bacterial genomes using CRISPR-Cas systems.     Nature biotechnology 31, 233-239 (2013). -   24. Pattanayak, V., Ramirez, C. L., Joung, J. K. & Liu, D. R.     Revealing off-target cleavage specificities of zinc-finger nucleases     by in vitro selection. Nature methods 8, 765-770 (2011). -   25. Schneider, T. D. & Stephens, R. M. Sequence logos: a new way to     display consensus sequences. Nucleic acids research 18, 6097-6100     (1990).

All publications, patents and sequence database entries mentioned herein, including those items listed above, are hereby incorporated by reference in their entirety as if each individual publication or patent was specifically and individually indicated to be incorporated by reference. In case of conflict, the present application, including any definitions herein, will control. 

What is claimed is:
 1. A method of selecting an RNA-programmable nuclease that specifically cuts a consensus target site from a plurality of nucleases, the method comprising (a) providing a plurality of candidate nucleases that cut the same consensus sequence; (b) for each of the candidate nucleases of step (a), identifying a nuclease target site cleaved by the candidate nuclease that differ from the consensus target site; and (c) selecting a nuclease based on the nuclease target site(s) identified in step (b).
 2. The method of claim 1, wherein identifying a nuclease target site comprises (i) contacting the nuclease with a library of candidate nucleic acid molecules, wherein each nucleic acid molecule comprises a concatemer of a sequence comprising a candidate nuclease target site and a constant insert sequence, under conditions suitable for the nuclease to cut a candidate nucleic acid molecule comprising a target site of the nuclease; and (ii) identifying nuclease target sites cut by the nuclease in (i) by determining the sequence of an uncut nuclease target site on the nucleic acid strand that was cut by the nuclease in step (i).
 3. The method of claim 1, wherein the nuclease selected in step (c) is the nuclease that cleaves the consensus target site with the highest specificity.
 4. The method of claim 3, wherein the nuclease that cleaves the consensus target site with the highest specificity is the candidate nuclease that cleaves the lowest number of target sites that differ from the consensus site.
 5. The method of claim 3, wherein the candidate nuclease that cleaves the consensus target site with the highest specificity is the candidate nuclease that cleaves the lowest number of target sites that are different from the consensus site in the context of a target genome.
 6. The method of claim 1, wherein the candidate nuclease selected in step (c) is a nuclease that does not cleave any target site other than the consensus target site.
 7. The method of claim 6, wherein the candidate nuclease selected in step (c) is a nuclease that does not cleave any target site other than the consensus target site within the genome of a subject at a therapeutically effective concentration of the nuclease.
 8. The method of claim 1 further comprising contacting a genome with the nuclease selected in step (c).
 9. The method of claim 8, wherein the genome is a vertebrate, mammalian, human, non-human primate, rodent, mouse rat, hamster, goat, sheep, cattle, dog, cat, reptile, amphibian, fish, nematode, insect, or fly genome.
 10. The method of claim 8, wherein the genome is within a living cell.
 11. The method of claim 8, wherein the genome is within a subject.
 12. The method of claim 1, wherein the consensus target site is within an allele that is associated with a disease or disorder.
 13. The method of claim 12, wherein cleavage of the consensus target site results in treatment or prevention of the disease or disorder.
 14. The method of claim 12, wherein cleavage of the consensus target site results in the alleviation of a symptom of the disease or disorder.
 15. The method of claim 12, wherein the disease is HIV/AIDS.
 16. The method of claim 15, wherein the allele is a CCRS allele.
 17. The method of claim 12, wherein the disease is a proliferative disease.
 18. The method of claim 17, wherein the allele is a VEGFA allele.
 19. An isolated nuclease that has been selected according to claim
 1. 20. The isolated nuclease of claim 19, wherein the nuclease has been engineered to cleave a target site within a genome.
 21. The isolated nuclease of claim 19, wherein the nuclease is a Cas9 nuclease comprising an sgRNA that is complementary to the target site within the genome.
 22. The isolated nuclease of claim 19, wherein the nuclease has been selected based on cutting no other candidate target site, not more than one candidate target site, not more than two candidate target sites, not more than three candidate target sites, not more than four candidate target sites, not more than five candidate target sites, not more than six candidate target sites, not more than seven candidate target sites, not more than eight candidate target sites, not more than eight candidate target sites, not more than nine candidate target sites, or not more than 10 candidate target sites in addition to its known nuclease target site. 